Wells finished the night 3-for-4, while Wells (5-5) scattered seven hits, walked one and struck out two as the Padres won for the second straight time after losing three in a row.
David Wright had three hits and scored for the NL East-leading Mets, who had a two-game winning streak broken. New York has dropped seven of its last nine road games.
Jorge Sosa (7-4) activated off the 15-day disabled list before the game, allowed five hits and two runs over six innings. Sosa, who had been out with a strained left hamstring, walked two and struck out four to lose for the third time in four decisions.