Arsenal's victory at the Emirates Stadium, thanks to goals from Tomas Rosicky, Cesc Fabregas, Thomas Vermaelen and Andriy Arshavin, lifted them above Chelsea on goals scored and put them top for the first time since August.
Arsenal have 48 points from 22 games, followed by Chelsea (48 from 21) and Manchester United (47 from 22).
Spurs are fourth on 38, but Liverpool, who moved up from seventh to sixth, are just a point behind them after two Dirk Kuyt goals gave them a victory to ease the pressure on beleaguered manager Rafa Benitez.
Bolton, deep in relegation trouble, stunned the home crowd when they deservedly doubled their advantage 20 minutes later, Denilson's sloppy tackle on Chung-Yong Lee leading to a penalty which Matt Taylor squeezed past the diving Manuel Almunia.
Arsenal grabbed one back just before halftime when neat footwork from captain Fabregas played in Rosicky who smashed home from inside the box. Arsenal equalised with a controversial goal after 52 minutes. Fabregas rode two tackles before calmly rolling the ball past goalkeeper Jussi Jaaskelainen.
Arsenal went ahead after 65 minutes when defender Vermaelen smashed home from a corner and Arsene Wenger's side added a fourth through Andriy Arshavin five minutes from time.