Jake Meyers ripped a two-run homer that cut the deficit to 6-5, and when pinch hitter Mauricio Dubon followed with a walk, Brandon Hughes (0-2) entered in relief of Thompson.
Mark Vientos, recalled earlier in the day from Triple-A Syracuse, hit a game-tying two-run homer in the seventh for the Mets.
Cardinals 3, Brewers 0Paul DeJong hit a two-run homer and Nolan Arenado delivered his 1,000th career RBI as St. Louis defeated visiting Milwaukee.
Boston tied its season high with 16 hits, including six in a six-run second inning.
Justin Turner went 3-for-4 with his second homer in as many games.