City are now two points ahead of the Toronto FC, with the top two clubs in each conference to go straight into the MLS Cup playoff semi-finals.
FIFA Council elections: Asian congress called off after 20 minutes
Villa notched his 20th goal of the season in the 52nd minute, receiving the ball from a corner kick from Italian midfielder Andrea Pirlo, making space and smashing a short angled shot into the net.
The Spanish striker added a goal in injury time and now has 21, one ahead of Bradley Wright-Phillips of the New York Red Bulls for the Golden Boot.
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