Leeds striker Luke Varney scored the only goal as Bolton slipped to their fourth successive league defeat.
It was the first time Leeds had opened the scoring in a league match this season as Varney headed home at the near post after just six minutes.
David Ngog and Darren Pratley both went close for the home side, but found Paddy Kenny in the Leeds goal in excellent form.
Defeat leaves Dougie Freedman's side joint bottom of the Championship table.
Bolton started the campaign among the favourites for promotion after just missing out on a place in last season's play-offs on goal difference.
However, so far this season they have managed just two points after draws with Burnley and Reading.
Jermaine Beckford, who scored 72 goals in 115 league starts for Leeds, was left on the bench by Bolton who at times looked devoid of ideas in attack.
Instead Ngog, who has scored only 11 goals in two years at Bolton, led the line.
In comparison Leeds boasted an attacking force of Ross McCormack, Varney and Noel Hunt.
The win for Leeds moves them up to sixth in the table, five points behind joint leaders Blackpool and Queens Park Rangers.
Bolton manager Dougie Freedman:
"Have we given up on automatic promotion? We'll never give up. Anything can happen in professional sport.
"Obviously we're disappointed with the result. To concede a goal after seven minutes was disappointing but we didn't have too many clear opportunities and that's the biggest disappointment.
"I'm certainly not worried because this is professional sport. You have your ups and downs but we've really got to start games better."
Leeds manager Brian McDermott:
"To come away and win 1-0 at Bolton is a great result.
"We're trying to get a group together that's difficult to play against but also we're trying to get a group that can control games better with the ball.
"We've been working at our set plays because they've been really important to us and it was a great delivery and a really good header from Luke (Varney)."