Phelps, who now has six homers with Durham, hit his first home run in the fourth inning to get the Bulls within 4-3.
However, Durham pitcher Jon Switzer (0-5) allowed three runs in the bottom of the fourth inning.
The Durham bullpen shut down the Indians the rest of the way, allowing just a single hit. Over the last two games, the Bulls' bullpen has thrown 11.1 scoreless innings, allowing only three hits.
Phelps hit his second home run in the eighth, another two-run shot to get the Bulls within two runs.
But Durham could not get a runner past second base after the homer by Phelps.
The Bulls, now 40-50, are in second place in the South Division, and eight-and-a-half games behind Norfolk with one game left before the All-Star Break.
Durham is 1-2 on a brief four-game road trip.
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