 McIlroy was confident of success after a 0-0 stalemate in the first leg |
Morecambe came from behind to book their place in the Conference play-off final with two Wayne Curtis goals. York went ahead through a Steve Bowey spot-kick after home goalkeeper Steve Drench had fouled Clayton Donaldson, dislocating his elbow in the process.
But the hosts responded well, Curtis meeting an Adam Yates free-kick with a looping header over City stopper Tom Evans before clipping in a second.
Sammy McIlroy's team will meet either Exeter or Oxford in the Wembley final.
However, after Bowey's 20th-minute opener Morecambe looked a long way from that 20 May date and a first play-off final at the third attempt.
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Drench and Donaldson clattered into each other on the edge of the area as they challenged for Manny Panther's long ball over the top and, after a lengthy delay, substitute keeper Scott Davies went the wrong way at the penalty.
But Evans gifted the Shrimps a way back into the game when he raced to the edge of his six-yard box and was caught in no-man's land as Curtis met a Yates free-kick from the right.
And shortly after the interval Curtis completed the comeback.
Evans twice blocked right-footed efforts from the striker on the left before Curtis opted for a cute, lofted finish off the outside of his left boot.