For each, it was their first homer of the 2013 season.
The Twins got off to a quick 3-0 lead in the first inning with RBI singles from Joe Mauer and Josh Willingham, combined with a RBI groundout by Oswaldo Arcia.
But the Marlins tied in up in the bottom of the fifth, with Mathis starting the scoring with a homer off starter Scott Diamond.
Diamond, who dropped to 5-7 on the year, cruised through four scoreless innings to start the game. But he didn't make it out of the sixth, charged with four runs on eight hits.
Diamond has failed to finish the sixth inning in eight of his last nine starts.
Ex-Twin Kevin Slowey, now in the Marlins bullpen, pitched three innings in relief to pick up the win for Miami.
While Minnesota struggled offensively again, Mauer did not. He picked up three more hits to improve his average to .337, second in the American League to Detroit's Miguel Cabrera.
The Twins now head back to Target Field for an eight-game homestand against Kansas City and the New York Yankees.