Substitute Raheem Sterling smashed home an 82nd-minute volley as City fought back for a 1-1 draw at Etihad Stadium after playing with 10 men for more than a half of a chaotic game on Monday.
The late equalizer slightly soured another landmark occasion for Rooney, the record scorer for England and United — and now only the second player to reach a double-century of Premier League goals after Alan Shearer.
Rooney scored Everton's goal against the run of play in the 35th minute, meeting Dominic Calvert-Lewin's cross with a first-time shot that struck City goalkeeper Ederson Moraes' heel and deflected into the net off the post.
City was already getting frustrated by its failure to pierce a deep-lying and compact Everton defense, and its chances of victory further receded in the 44th when right back Kyle Walker was sent off for a second yellow card in the space of two minutes.
And after smashing a glaring opportunity over the bar from close range, he made amends by meeting Holgate's poor headed clearance with a sweetly struck left-footed volley from just inside the area.
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