Everton delivered a blow to Arsenal's title ambitions as Tomasz Radzinski snatched a hard-earned point.
Kanu's first-half goal ensured Arsene Wenger's side maintained their unbeaten start to the league season after a stormy Goodison Park encounter.
But Radzinski struck with 15 minutes left to level for Everton after a mistake by Arsenal's Ashley Cole.
Arsenal had chances of their own to snatch victory, but that would have been harsh on David Moyes' men.
Everton boss Moyes opted for an attacking formation, with influential midfielder Thomas Gravesen ruled out with a knee injury.
Rooney joined Duncan Ferguson and Radzinski as Everton attempted to stop Arsenal's Premiership bandwagon in its tracks.
And Rooney was involved as Everton almost broke the deadlock after 16 minutes, when his corner unwittingly rebounded off Kevin Kilbane and was scrambled off the line by Cole.
29 mins: Kanu gives Arsenal the lead
75 mins: Radinski stretches to level for Everton
Kolo Toure was left limping as tackles flew in, and despite struggling on, he was replaced by Lauren in the 21st minute.
Arsenal survived a spell of pressure and went ahead eight minutes later through Kanu.
Thierry Henry slipped the ball through a square, slow back line and the Nigerian was on to it in a flash to slip round Martyn and slide home his first league goal of the season.
But Rooney wasted a glorious chance to equalise seven minutes before half-itime when he somehow headed wide from six yards from a perfect Kilbane cross.
Everton needed to exert more control in midfield, and it was no surprise when Li Tie was replaced by Tobias Linderoth at the start of the second half.
And Rooney almost made up for his earlier miss when, after Ray Parlour fouled Kilbane and Freddie Ljungberg had been booked for dissent, the teenager saw his free-kick brilliantly saved by Jens Lehmann.
Henry was threatening to catch Everton on the break with his lightning pace, and twice he almost created the chances to double Arsenal's advantage.
And with 20 minutes remaining, Everton sent on Francis Jeffers, on loan from Arsenal for the season, for the injured Kilbane.
Jeffers was involved as Everton deservedly equalised after 75 minutes.
He pounced on an error by Cole, and when Lehmann saved his shot Radzinski stretched to score.
Everton: Martyn, Hibbert, Stubbs, Unsworth, Naysmith, Rooney, Carsley, Li Tie (Linderoth 45), Kilbane (Jeffers 70), Radzinski (Campbell 87), Ferguson.
Subs Not Used: Simonsen, Yobo.
Arsenal: Lehmann, Toure (Lauren 20), Cygan, Campbell, Cole, Ljungberg (Silva 89), Parlour, Vieira, Pires, Kanu (Edu 81), Henry.
Subs Not Used: Shaaban, Aliadiere.
Booked: Parlour, Lauren, Ljungberg.
Referee: A Wiley (Staffordshire).