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Alfaro went deep to center field on the first pitch he saw from Cole Sulser (0-1), sending Petco Park into a frenzy and earning him a curtain call. He was purchased from the Marlins for cash in December.
Until the ninth, it appeared that the Padres were headed for a second straight shutout. But Trent Grisham and CJ Abrams got on base ahead of Alfaro, who tossed his bat aside and brushed one hand across the “Padres” on the front of his jersey before starting his trot. It was his second homer.
Jazz Chisholm homered for the Marlins, who have lost seven of eight games.
Manny Machado extended his on-base streak to 18 games, but neither he nor Eric Hosmer — two of the best hitters in baseball this season — could deliver a big blow for the Padres.
Rogers got Hosmer to pop up with two runners on to end both the third and fifth innings. After Kim Ha-seong hit a fly ball to the warning track in the left-field corner for the second out in the fifth with a runner on, Machado drove a ball down the line that curved foul then singled before Hosmer popped up.
Machado was batting .381 and Hosmer .355 coming in. The next-best Padres regular was batting .238, and four were below .200.
Rogers held San Diego to five hits in five innings while striking out three and walking two.
San Diego’s Joe Musgrove threw a season-high 108 pitches in seven strong innings. He held the Marlins to two runs and five hits while striking out eight and walking one. Robert Suarez (2-1) got the win for the Padres, working two innings with a strikeout and no hits.
Marlins: Placed LHP Richard Bleier on the injured (undisclosed) and selected INF Erik Gonzalez from Triple-A Jacksonville.
Marlins: RHP Elieser Hernandez (2-1, 6.66) is scheduled to start Monday night in the opener of a three-game series at Arizona, which will counter with RHP Humberto Castellanos (2-1, 4.12).
Padres: Rookie LHP MacKenzie Gore (2-0, 1.71) is scheduled to start Monday night in the opener of a three-game home series against RHP Kyle Hendricks (1-3, 5.64) and the Chicago Cubs.