Chelsea's shock 1-0 defeat at Crystal Palace earlier in the day meant victory for City would see them sitting at the summit on goal difference.
And that looked set to come to fruition as David Silva deservedly broke the deadlock in the 18th minute, with City dominating the first half at the Emirates Stadium.
City are now two points adrift of leaders Chelsea, over whom they have two games in hand, and one behind Liverpool, who have played one game more than Manuel Pellegrini's men.
Tomas Rosicky went down under the challenge of Pablo Zabaleta in the penalty area 12 minutes in, but referee Mike Dean waved away Arsenal's protests, with replays suggesting that it was probably the correct call.
Silva's opener capped a swift counter-attacking move from City – the Spaniard tapping home from close range after Edin Dzeko had rifled an effort against the left-hand post.
Samir Nasri – booed and heckled throughout on his former stomping ground – was next to have a pop at goal, but his tame attempt was comfortably collected by Arsenal stopper Wojciech Szczesny.
The face of the game changed eight minutes into the second half when Flamini atoned for his midweek misfortune by diverting Lukas Podolski's cross into the back of the net from a central position in the penalty area, drawing Arsenal level with his second goal since returning to the club last year.
Arsenal were unable find a winner, but a point against the title favourites will come as a relief to manager Arsene Wenger, who has endured a difficult week after marking 1,000 games in charge with a 6-0 defeat at Chelsea last weekend, and will go some way to easing the pain of the 6-3 loss in December's reverse fixture.
