The former Manchester United forward, who predictably had every touch booed by the home supporters, fired Everton in front 10 minutes before half-time to bring up his double-century in the competition, becoming only the second player to reach the milestone after Alan Shearer.
However, Everton left Manchester disappointed to take only a point after Raheem Sterling struck late on to deny Ronald Koeman's men a rare Etihad win.
The Toffees - leading through Rooney's second strike of the campaign - were aided by a controversial red card for Kyle Walker just before the break.
City had been building momentum prior to the opening goal and then recovered well before Walker clashed with Dominic Calvert-Lewin - a soft second bookable offence leaving the hosts a man down for the entire second half.
But Pep Guardiola's men kept pushing and, after a series of squandered chances, Sterling blasted an 82nd-minute equaliser to keep City unbeaten at this early stage of the season.
Both teams ended the game with 10 men as Morgan Schneiderlin - initially booked in the seventh minute - joined Walker in earning a second card in the closing stages.
After 22 minutes and only a Calvert-Lewin half-chance for Everton, supporters of both teams joined in applause to commemorate the victims of recent terror attacks in Manchester and Barcelona.
City tested Jordan Pickford shortly afterwards with Nicolas Otamendi stepping up to shoot hard and low, the goalkeeper parrying to Sergio Aguero whose delicate finish on the rebound was nodded clear by Phil Jagielka.
More superb Jagielka defending closed down the angle for Aguero just as he looked to have wriggled clear and, with the pressure building, David Silva's drive then rattled the foot of the left-hand post.
But Rooney's moment arrived less than a minute later, ghosting into the area to meet Calvert-Lewin's pass and slot home a finish via both Ederson and the upright.
As City sought a riposte, Rooney was fortunate to see Gabriel Jesus scuff straight at Pickford after a sloppy giveaway.
But the game turned further in Everton's favour on the stroke of half-time when Walker, already booked, barged into Calvert-Lewin as the pair tussled for a high ball and earned a contentious second yellow from referee Bobby Madley.
City again took control after the restart, but visiting manager Ronald Koeman responded with two positive changes - bringing on Davy Klaassen and debutant Gylfi Sigurdsson - to feed Calvert-Lewin's tireless running and retain a threat on the counter-attack.
Guardiola's own substitutes made an impact, too, though, with Bernardo Silva and Sterling shooting off target from good positions in the area before Pickford saved well from Danilo.
But Everton could not hold out and Mason Holgate's poor header from an angled cross fell kindly for Sterling to thrash a volley beyond Pickford and earn a hard-fought point.
Schneiderlin then followed Walker down the tunnel as he flew into a challenge on Aguero, although he appeared to take the ball, and it was the visitors who ended the game desperate for the final whistle.
Key Opta stats:
- Wayne Rooney scored his 200th Premier League goal in this match – the only player with more in the competition is Alan Shearer (260).
- Rooney has now scored nine Premier League goals versus Man City; only Alan Shearer has more against them in the competition (11).
- Rooney has now scored in five of his last eight Premier League appearances.
- Manchester City defender Kyle Walker’s two yellow cards were just one minute and 57 seconds apart in this match.
- It was Walker’s first-ever Premier League red card in what was his 200th appearance in the competition.
- Everton are the first opposition team that Pep Guardiola has failed to beat within his first three league meetings as a manager.