The match official dismissed City's Shaun Wright-Phillips for tripping Everton's Gary Naysmith.
It was a blatant penalty, but Naysmith was not in a clear goalscoring position, though Knight later confirmed it was for a professional foul.
City manager Kevin Keegan said that they will be hoping to overturn the decision following an appeal.
"It was a clear penalty and booking, but it did not warrant a sending-off, and I do not know any other referee who would have sent the player off," explained Keegan.
The City chief was delighted to see Anelka finally get off the mark, though it was not his goal which impressed him most: "Anelka gave us so much energy and what I remember most was him chasing back 60 yards on one occasion to make a challenge," explained Keegan.
But even though City were down in numbers for more than an hour they emerged the victors. David Unsworth halved Everton's deficit with the penalty which had been conceded by Wright-Phillips as Everton were handed an unexpected lifeline.
City were forced to fight a defensive rearguard action in the second half with keeper Peter Schmeichel saving superbly to deny Nicals Alexandersson, Kevin Campbell and Unsworth, but in the dying minutes Anelka robbed Naysmith and broke away to complete his treble and seal victory.