The England centre-back lost his marker at the back post to guide home Phil Foden’s searching left wing free kick inside the opening five minutes of the second half.
Stones had been thankful for an offside decision just three minutes into the game when Zack Steffen’s save from a Marcus Rashford drive inadvertently rebounded off him and into the net.
It was a similar story at the other end too, with Ilkay Gundogan and Foden both having goals chalked off before the half hour when the flag was raised.
But it was Kevin De Bruyne who went closest to finding the breakthrough in an end to end first half, driving a stinging effort against the post from the edge of the box after being fed in by Raheem Sterling in the 13th minute.
City were quickest out of the blocks in the second 45 and were rewarded when Foden’s searching free-kick from the left found Stones, who reacted quickest to guide the ball home past Henderson.
And after some inspired goalkeeping from Dean Henderson to deny Sterling and Riyad Mahrez in particular it took a moment of individual brilliance to put the game to bed.
The hosts failed to properly clear a right wing corner and paid the price when an unmarked Fernandinho drove a rasping low volley into the bottom corner of the net from the edge of the box with less than ten minutes to go.
A complete performance from City secured with a goal of true quality, Tottenham Hotspur await in the final at the end of April!
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