The Padres responded with six runs in the fourth, highlighted by Cameron Maybin's three-run homer and back-to-back, RBI triples from Alexi Amarista and Will Venable.
It stayed that way until Phillips belted a one-out, 2-0 pitch from Jason Marquis (4-6) into the left field stands for the go-ahead tally in the seventh.
The hit made a winner of Sean Marshall (4-3), who hurled two scoreless frames, while Aroldis Chapman tossed a 1-2-3 ninth for his 22nd save as National League Central-leading Cincinnati won for the 11th time in 12 games.
Marquis was tagged for seven runs on eight hits over 6 1/3 innings for San Diego.
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