The former Valencia, Barcelona and Atletico Madrid forward had created his new team's debut MLS goal in a 1-1 draw last week, and led the way again at Yankee Stadium, inspiring New York to a 2-0 triumph over New England Revolution.
Villa put his name in the record books with a well-taken goal in the first half and then crossed for Patrick Mullins to wrap up New York's win with six minutes remaining.
After Sebastian Velasquez and Mix Diskerud combined to win the ball in midfield for New York in the 19th minute, Ned Grabavoy surged into the home side's attacking half before feeding Villa on the left wing.
With space to run at New England's defence, Villa drove towards goal, played a neat one-two with Grabavoy and then curled his right-footed shot around Revolution goalkeeper Bobby Shuttleworth and inside the far post.
The Spaniard, who lined up in a front two with Adam Nemec, created the hosts' second goal from the left as well, holding off Scott Caldwell on a counter-attack before teeing up Mullins at the back post for a tap-in.
The victory took New York to the top of the MLS' Eastern Conference ahead of fellow newcomers Orlando City.
Also on Sunday, Portland Timbers had looked set to avoid yet another draw at home before Alan Gordon struck in stoppage time for champions Los Angeles Galaxy in a 2-2 stalemate.
Fanendo Adi had twice given the Timbers the lead at Providence Park, with his second goal coming in the 90th minute, but Gordon's header two minutes later saw Portland draw their third straight game at home.
Gyasi Zardes scored the Galaxy's other goal to level at 1-1 in the 65th minute.
Portland started last season with seven draws in their opening nine home games.
