Eovaldi (2-6), obtained by the Marlins this week as part of the trade that sent Hanley Ramirez to the Los Angeles Dodgers, limited the Padres to one run over 5 1/3 innings, walking two and fanning five.
He singled to lead off the third and two outs later came home to score on a two-run shot from Reyes, which handed Miami a 3-0 advantage.
Edward Mujica and Mike Dunn combined to hold San Diego to one run over 2 2/3 relief innings and Steve Cishek notched his fourth save as the Marlins evened their three-game series.
San Diego's Ross Ohlendorf (3-1) absorbed the loss, allowing three runs on four hits in a six-inning effort.
Yonder Alonso and Yasmani Grandal knocked in runs for the Padres.
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