Mark Davies' strike sealed Bolton's first away league win of the season at Sheffield Wednesday's expense.
The midfielder netted after a mazy run, beating three players before smashing a shot into the top corner of the net.
The visitors went ahead on the stroke of half-time through Marcos Alonso who scored after some sloppy defending.
On-loan Everton man Ross Barkley had restored parity with a penalty after Anthony Gardner was fouled in the box, but Davies was the match winner.
The loss represents just seven points picked up from seven games for Dave Jones's side, their worst start to a league season in five years.
99th league meeting since 1892
Sheffield Wednesday wins: 43
Bolton wins: 35
Their second home defeat means they have now equalled the total number of losses suffered at Hillsborough last season and they started the match on the back foot as Bolton winger Chris Eagles came close with two efforts, one struck wide and a lob that just went over the bar.
It was the former Manchester United man who provided the first goal, as his corner was headed home by Spaniard Alonso.
Wednesday, whose own Spanish player Rodri forced a good save from Adam Bogdan, were given the chance to draw level as Gardner was brought down in the area by Keith Andrews, and Barkley confidently tucked home the penalty just after the hour mark.
Minutes later though, Davies took centre stage after being given the ball by namesake Kevin, he embarked on a solo run which left Wednesday defenders floundering and a shot that goalkeeper Chris Kirkland had no chance of saving.
The home side's best chance of a second equaliser fell to Slovenian Nejc Pecnik but his 20-yard volley sailed over the bar as the Trotters secured their fifth successive victory in league and cup against the Owls.
Sheffield Wednesday boss Dave Jones:
"Our lads feel that every mistake we make at the moment is being punished.
"We had three or four chances to clear both goals, but we didn't and we have been punished. That is the level we are playing at - we can't keep giving the opposition easy chances to score.
"I felt we worked hard but we have to learn not to switch off. It's a tough learning curve.
"We have a lot of young players at the club and we can't get our heads down. We have to stay strong, keep plugging away and hopefully we can turn this run around.
"If fans thought we were going to come into this division and take it by storm they are kidding themselves. It's a building process and we are just at the start of that."
Bolton boss Owen Coyle:
"When you come to a stadium like Hillsborough, with the huge crowd, you know it's going to be difficult. So for us to put on a performance like that, I thought we were terrific.
"It would have been easy for our players to feel sorry for themselves when they got it back to 1-1 - from a penalty that I thought was debatable.
"It didn't affect us, though. We picked ourselves up and scored a quality winning goal.
"We've scored two goals today and we could have had five or six. Nobody who witnessed that game can argue that the better team won and that we gave a great performance, so we can take confidence from that and now kick on."
Full Time The referee signals the end of the game.
Ross Barkley has an effort at goal from 30 yards. Save made by Adam Bogdan.
90:00 +1:56 Substitution
Substitution (Bolton) makes a substitution, with Darren Pratley coming on for Keith Andrews.
Foul by Benik Afobe on Chris O'Grady, free kick awarded. Daniel Jones restarts play with the free kick.
The ball is delivered by Chris O'Grady.
Foul by Kevin Davies on Anthony Gardner, free kick awarded. Chris Kirkland restarts play with the free kick.
Nejc Pecnik produces a right-footed shot from just outside the area that goes harmlessly over the bar.
The ball is swung over by Mark Davies.
Jose Semedo challenges Chris Eagles unfairly and gives away a free kick. Indirect free kick taken by Tyrone Mears.
Nejc Pecnik takes a inswinging corner from the left by-line played to the near post.
Free kick awarded for an unfair challenge on Keith Andrews by Ross Barkley. Direct free kick taken by Chris Eagles. Chris Eagles takes a shot from just outside the penalty area clears the crossbar.
Inswinging corner taken by Nejc Pecnik.
Inswinging corner taken by Chris Eagles from the left by-line played to the near post, clearance by Nejc Pecnik.
Substitution Chris O'Grady joins the action as a substitute, replacing Jay Bothroyd.
Centre by Michail Antonio.
Benik Afobe takes a shot. Save by Chris Kirkland. Corner taken by Chris Eagles.
Effort from outside the area by Ross Barkley goes wide right of the goal. Corner taken right-footed by Nejc Pecnik from the left by-line, Header from close range by Michail Antonio misses to the right of the target.
Free kick awarded for an unfair challenge on Ross Barkley by Keith Andrews. Kieran Lee takes the free kick.
Substitution David Ngog leaves the field to be replaced by Benik Afobe.
Assist by Kevin Davies.
64:32 Goal scored
Goal - Mark Davies - Sheff Wed 1 - 2 Bolton Goal scored by Mark Davies from the edge of the penalty box to the top left corner of the goal. Sheff Wed 1-2 Bolton.
Unfair challenge on Kevin Davies by Anthony Gardner results in a free kick. Chris Eagles takes the free kick.
Jay Bothroyd is ruled offside. Adam Bogdan restarts play with the free kick.
61:28 Goal scored
Goal - Ross Barkley - Sheff Wed 1 - 1 Bolton Penalty taken right-footed by Ross Barkley and scored. Sheff Wed 1-1 Bolton.
Booking The referee shows Zat Knight a yellow card for dissent.
Penalty awarded for a foul by Keith Andrews on Anthony Gardner.
Inswinging corner taken left-footed by Daniel Jones from the right by-line. Nejc Pecnik takes a outswinging corner.
Booking The referee shows Tyrone Mears a yellow card.
Tyrone Mears concedes a free kick for a foul on Jermaine Johnson. Nejc Pecnik restarts play with the free kick.
Substitution Jermaine Johnson replaces Lozano Rodri.
Jay Bothroyd gives away a free kick for an unfair challenge on Matt Mills. Tyrone Mears takes the indirect free kick.
Marcos Alonso crosses the ball.
Inswinging corner taken by Chris Eagles, Centre by Mark Davies. Chris Eagles takes a shot. Nejc Pecnik gets a block in. Corner from right by-line taken by Chris Eagles.
Free kick awarded for a foul by Kevin Davies on Ross Barkley. Chris Kirkland restarts play with the free kick.
Kevin Davies gives away a free kick for an unfair challenge on Anthony Gardner. Chris Kirkland takes the free kick.
Matt Mills fouled by Jay Bothroyd, the ref awards a free kick. Free kick taken by Adam Bogdan.
Booking Jay Spearing shown a yellow card.
Booking Lozano Rodri is shown a yellow card for dissent.
Free kick awarded for an unfair challenge on Lozano Rodri by Jay Spearing. Daniel Jones takes the free kick.
Corner taken by Chris Eagles, Jay Bothroyd manages to make a clearance.
The ball is crossed by Kevin Davies, Anthony Gardner makes a clearance.
Ross Barkley takes a shot. Blocked by Jay Spearing.
Jay Bothroyd fouled by Keith Andrews, the ref awards a free kick. Kieran Lee takes the free kick.
The referee starts the second half.
Substitution Jose Semedo is brought on as a substitute for Rhys McCabe.
45:00 +2:21 Half time
Half Time It is the end of the first-half.
Lozano Rodri takes a shot. Save by Adam Bogdan.
Kieran Lee takes a shot. Blocked by Keith Andrews.
Rhys McCabe crosses the ball from the free kick right-footed from right wing, Marcos Alonso manages to make a clearance. Inswinging corner taken from the right by-line by Rhys McCabe, clearance by David Ngog.
Booking Marcos Alonso receives a yellow card for unsporting behaviour.
Marcos Alonso concedes a free kick for a foul on Michail Antonio.
Assist on the goal came from Chris Eagles.
43:10 Goal scored
Goal - Marcos Alonso - Sheff Wed 0 - 1 Bolton Marcos Alonso grabs a headed goal from deep inside the penalty area. Sheff Wed 0-1 Bolton.
Effort from 12 yards by Chris Eagles. Daniel Jones gets a block in. Outswinging corner taken right-footed by Chris Eagles,
Shot on goal by David Ngog from just inside the area clears the crossbar.
Free kick awarded for a foul by Keith Andrews on Rhys McCabe. Indirect free kick taken by Anthony Gardner.
Rhys McCabe takes a shot from just outside the penalty area which clears the crossbar.
Marcos Alonso takes a shot from 35 yards and missed to the right of the target.
Outswinging corner taken from the left by-line by Chris Eagles, Nejc Pecnik manages to make a clearance.
Free kick awarded for a foul by Marcos Alonso on Michail Antonio. Direct free kick taken by Rhys McCabe.
Shot from deep inside the area by Chris Eagles goes over the bar.
Daniel Jones produces a cross, Zat Knight makes a clearance.
The offside flag is raised against Lozano Rodri. Adam Bogdan restarts play with the free kick.
Centre by David Ngog. Effort on goal by Chris Eagles from inside the penalty box misses to the right of the target.
Marcos Alonso crosses the ball.
Chris Eagles has an effort at goal from outside the penalty box which goes wide right of the target. Outswinging corner taken by Chris Eagles.
Free kick awarded for an unfair challenge on Jay Bothroyd by Marcos Alonso. Daniel Jones restarts play with the free kick.
The ball is swung over by Michail Antonio, Matt Mills makes a clearance.
Michail Antonio takes a shot. Save by Adam Bogdan.
Tyrone Mears restarts play with the free kick.
Booking Rhys McCabe receives a caution for unsporting behaviour.
Rhys McCabe gives away a free kick for an unfair challenge on Tyrone Mears.
Jay Spearing concedes a free kick for a foul on Jay Bothroyd. Direct strike on goal from the free kick comes in from Rhys McCabe. Inswinging corner taken by Rhys McCabe, clearance made by Marcos Alonso.
The ball is sent over by David Ngog, save made by Chris Kirkland.
Unfair challenge on Anthony Gardner by David Ngog results in a free kick. Chris Kirkland restarts play with the free kick.
Outswinging corner taken from the right by-line by Chris Eagles, clearance made by Jay Bothroyd.
Ross Barkley concedes a free kick for a foul on Jay Spearing. Keith Andrews restarts play with the free kick.
Daniel Jones takes a inswinging corner from the right by-line played to the near post, clearance made by David Ngog.
The ball is swung over by Michail Antonio, clearance by Zat Knight.
The ball is swung over by Tyrone Mears, Chris Eagles takes a shot. Save made by Chris Kirkland.
Martin Taylor challenges Kevin Davies unfairly and gives away a free kick. Keith Andrews takes the free kick.
Michail Antonio produces a cross.
Marcos Alonso challenges Jay Bothroyd unfairly and gives away a free kick. Kieran Lee takes the free kick.
The game gets underway.
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