Mercer circled the bases in the second inning for a 2-0 Pirates lead when Reds right-fielder Jay Bruce made a dive for his liner but missed, allowing it to roll to the wall.
Jones added a solo shot in the eighth for Pittsburgh, which will host the Reds in Tuesday's National League wild-card game -- its first home post-season game since 1992.
Brandon Cumpton (2-1) allowed two hits over five scoreless innings as the Pirates (94-68) swept the three-game series against their division rival.
Greg Reynolds (1-3) yielded three runs on seven hits over five innings for the Reds (90-72), who enter the playoff contest with a five-game losing streak.
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