Jack Hannahan drew a one-out walk in the 13th, reached third on a double by Shin-Soo Choo and came in when Votto lifted a fly ball to left.
San Diego had a 3-1 lead going into the eighth, but with one away Kennedy allowed an infield single to Zack Cozart and then gave up a home run to Xavier Paul.
It was the third pinch-hit home run of the season for Paul. Until that inning, Kennedy had surrendered only one hit and two walks.
The win went to Sam LeCure (2-1), the sixth Cincinnati pitcher who allowed one hit in the final 1 1/3 innings.
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