Springs scattered three hits, struck out seven and walked three while logging seven innings.
The Astros rallied in the ninth on Jeremy Pena's two-run homer against Jovani Moran.
Adam Duvall blasted a two-run homer and a pair of doubles while scoring three times.
Pete Alonso and Eduardo Escobar each hit two-run homers for the Mets, who have won five of six games against the Marlins.
Perdomo had three RBIs and two hits as Arizona racked up season highs for runs and hits (17).