Church had not played since June 6 because of the effects of his second concussion this year. He was activated from the disabled list and recently acquired outfielder Trot Nixon went on the 15-day DL with a strained groin.
Church batted sixth and played right field against the Yankees. Over the last month, he had been slowed by dizziness, had trouble with bright light and felt uncomfortable on team flights.
Obtained from the Washington Nationals in an offseason trade, Church had been among the Mets' most consistent players before his latest injury. He was hitting .300 with 10 home runs and 35 RBI going into the wrapup of the Subway Series.
Church was initially hurt in a spring training collision with teammate Marlon Anderson. Then on May 20 at Atlanta, he was accidentally kneed in the head by Braves shortstop Yunel Escobar while trying to break up a game-ending double play.
Church pinch-hit on May 22, but did not start again until June 1. Still not feeling 100 percent, he went 0-for-4 with three strikeouts on June 6 at San Diego.
After that game, the Mets put him on the DL with post-concussion syndrome.
Church played two rehab games last week with Class A Brooklyn, going 3-for-6 overall.
The Mets acquired Nixon on June 13 in a trade with Arizona to help with their depleted outfield. He hit .171 with one home run in 35 at-bats with New York.