Villa, on a 10-game loan spell from New York City, came off the bench in the 48th minute and pulled Melbourne level after collecting the ball and firing a low shot from the edge of the area past Sydney goalkeeper Vedran Janjetovic.
It was Villa's first match since scoring for Spain in a 3-0 rout of Australia as both sides exited the World Cup at the group stage in June.
Former Barcelona and Valencia forward Villa, Spain's all time leading scorer, received warm applause upon his arrival from the 25,000 fans but was quiet after his neat goal.
City, formerly Melbourne Heart but rebranded after their purchase by English champions Manchester City, had the best of the game but Mate Dugandzic was particularly wasteful.
The Melbourne club gave a debut to former Ireland international Damien Duff but were without their other marquee signing, Slovenian midfielder Robert Koren, because of a calf injury.
Sydney, who took the lead in the 55th minute after a curling effort from Corey Gameiro, almost won the game but Terry Antonis's stunning 30 metre strike in the dying minutes rattled the crossbar and substitute Max Burgess wasted the rebound.
On Friday, AFC Champions League finalists Western Sydney Wanderers were brought crashing back to earth after their continental success when they opened with a 4-1 thrashing at Melbourne Victory.
Defending champions Brisbane Roar open their campaign on Sunday at home to Adelaide United.
(Writing by Patrick Johnston in Singapore; Editing by John O'Brien)
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