Referee Mark Clattenburg played the advantage after Gretar Steinsson's challenge on Gervinho and Aaron Ramsey fed Van Persie, who shot low past Jaaskelainen.
Seeking a first league win at Arsenal since 1962, Bolton's task was made considerably harder when Wheater - deputising for the unwell Gary Cahill, a summer target for Arsenal - was sent off for pulling Walcott down as he ran clear.
Coyle frustrated by lapses and red card
The hosts began pouring forward and were it not for the hands of Jaaskelainen, they would have certainly extended their advantage.
As the game opened up, Bolton squandered a fine opportunity to equalise - Chris Eagles shooting straight at Szczesny - but then back came Arsenal.
After several near misses, Van Persie finally reached three figures by turning in Walcott's cross before Jaaskelainen saved from Walcott when one-on-one.
Late on, Song collected Bacary Sagna's cut-back and whipped home a high finish - but Walcott's late injury took some of the gloss off what was only Arsenal's second win of the campaign.
Full Time The final whistle goes and the game is over.
Effort from inside the area by Andrey Arshavin misses to the right of the goal.
Nigel Reo-Coker takes a shot. Blocked by Alex Song. Martin Petrov takes a inswinging corner from the right by-line played to the near post, Marouane Chamakh manages to make a clearance.
Bacary Sagna provided the assist for the goal.
88:15 Goal scored
Goal - Alex Song - Arsenal 3 - 0 Bolton Alex Song gets on the score sheet with a goal from inside the area to the top right corner of the goal. Arsenal 3-0 Bolton.
Substitution Marouane Chamakh joins the action as a substitute, replacing Robin van Persie.
Effort from the edge of the area by Theo Walcott goes wide of the right-hand post.
Robin van Persie takes a shot. Zat Knight gets a block in. Andrey Arshavin takes a short corner. Aaron Ramsey has an effort at goal from outside the box which misses left.
Robin van Persie takes the inswinging corner, Kevin Davies manages to make a clearance.
Free kick taken by Wojciech Szczesny.
Substitution Tomas Rosicky replaces Mikel Arteta.
The official flags Kevin Davies offside.
Unfair challenge on Robin van Persie by Mark Davies results in a free kick. Aaron Ramsey takes the direct free kick.
Substitution Andrey Arshavin replaces Yao Gervinho.
Theo Walcott takes a shot. Save made by Jussi Jaaskelainen.
Aaron Ramsey takes a shot. Save by Jussi Jaaskelainen.
Unfair challenge on Mark Davies by Mikel Arteta results in a free kick. Free kick taken by Gretar Rafn Steinsson.
Assist by Theo Walcott.
70:41 Goal scored
Goal - Robin van Persie - Arsenal 2 - 0 Bolton Robin van Persie scores a goal from inside the six-yard box low into the middle of the goal. Arsenal 2-0 Bolton.
Substitution (Bolton) makes a substitution, with Mark Davies coming on for Chris Eagles.
Robin van Persie takes a shot. Save by Jussi Jaaskelainen. Short corner taken by Aaron Ramsey from the left by-line. Laurent Koscielny takes a shot. Save by Jussi Jaaskelainen. Short corner taken by Robin van Persie from the right by-line.
Chris Eagles takes a shot. Save by Wojciech Szczesny. Shot from just outside the area by Robin van Persie misses to the left of the target.
Mikel Arteta has a drilled shot. Save made by Jussi Jaaskelainen. Short corner worked by Mikel Arteta. Bacary Sagna takes a shot. Dedryck Boyata gets a block in.
Free kick awarded for a foul by Aaron Ramsey on Darren Pratley. Free kick taken by Zat Knight.
Mikel Arteta has an effort at goal from the edge of the box that misses to the right of the target. Inswinging corner taken by Robin van Persie from the right by-line, Dedryck Boyata makes a clearance.
Booking Gretar Rafn Steinsson is shown a yellow card.
Robin van Persie has a direct shot on goal from the free kick, Jussi Jaaskelainen makes a save.
Substitution Fabrice Muamba goes off and Dedryck Boyata comes on.
Dismissal The referee red cards David Wheater for professional foul.
David Wheater gives away a free kick for an unfair challenge on Theo Walcott.
Theo Walcott takes a shot. David Wheater gets a block in.
Foul by Yao Gervinho on Nigel Reo-Coker, free kick awarded. Paul Robinson restarts play with the free kick.
Robin van Persie challenges Chris Eagles unfairly and gives away a free kick. Direct free kick taken by Jussi Jaaskelainen.
Robin van Persie takes a shot. Save made by Jussi Jaaskelainen.
The assist for the goal came from Aaron Ramsey.
45:36 Goal scored
Goal - Robin van Persie - Arsenal 1 - 0 Bolton Robin van Persie gets on the score sheet with a goal from inside the area to the bottom left corner of the goal. Arsenal 1-0 Bolton.
The second half has started.
45:00 +1:59 Half time
Half Time The ref blows to signal half-time.
Theo Walcott has an effort at goal from outside the penalty box missing to the wide right of the target.
Corner taken by Robin van Persie from the right by-line played to the near post, clearance by Kevin Davies.
Unfair challenge on Nigel Reo-Coker by Alex Song results in a free kick. Free kick taken by Jussi Jaaskelainen.
Theo Walcott takes a shot. Paul Robinson gets a block in.
Fabrice Muamba challenges Yao Gervinho unfairly and gives away a free kick. Laurent Koscielny restarts play with the free kick.
Laurent Koscielny produces a volleyed left-footed shot from deep inside the penalty box which goes wide of the left-hand upright.
Effort on goal by Yao Gervinho from just outside the penalty area goes harmlessly over the target.
The official flags Darren Pratley offside. Indirect free kick taken by Wojciech Szczesny.
Theo Walcott is ruled offside. Free kick taken by Jussi Jaaskelainen.
Kevin Davies challenges Per Mertesacker unfairly and gives away a free kick. Direct free kick taken by Laurent Koscielny.
Free kick awarded for a foul by Bacary Sagna on Darren Pratley. Jussi Jaaskelainen restarts play with the free kick.
Inswinging corner taken from the left by-line by Mikel Arteta, save made by Jussi Jaaskelainen.
Kevin Davies gives away a free kick for an unfair challenge on Alex Song. Free kick taken by Bacary Sagna.
Free kick awarded for a foul by Fabrice Muamba on Aaron Ramsey. Direct free kick taken by Aaron Ramsey.
Substitution David Ngog leaves the field to be replaced by Kevin Davies.
The offside flag is raised against Robin van Persie. Jussi Jaaskelainen takes the indirect free kick.
Inswinging corner taken by Mikel Arteta, clearance made by Paul Robinson.
Robin van Persie fouled by David Wheater, the ref awards a free kick. Free kick taken by Bacary Sagna.
The assistant referee flags for offside against David Ngog. Free kick taken by Wojciech Szczesny.
Free kick awarded for a foul by David Wheater on Theo Walcott. Mikel Arteta takes the free kick. Shot from outside the box by Robin van Persie misses to the left of the goal.
Free kick awarded for a foul by Darren Pratley on Aaron Ramsey. Free kick taken by Mikel Arteta.
Handball decision goes against Yao Gervinho. Chris Eagles crosses the ball in from the free kick, Alex Song makes a clearance.
Darren Pratley takes a shot. Save made by Wojciech Szczesny. Corner taken by Martin Petrov from the right by-line to the near post, clearance by Robin van Persie.
Free kick awarded for a foul by Laurent Koscielny on David Ngog. Free kick taken by Martin Petrov.
The ref blows the whistle to begin the match.
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