Jones was making his first appearance of 2012 after undergoing surgery late last month to repair a torn meniscus in his left knee.
His blast capped a three-run third inning, during which Dan Uggla also stroked an RBI double, and Tyler Pastornicky later added a solo shot as the Braves improved to 1-4.
Tommy Hanson (1-1) struck out eight over five innings, surrendering two runs on six hits and three walks.
Astros starter Kyle Weiland (0-1) was touched for four runs on eight hits over five frames.
Carlos Lee went 3-for-3 with two run-scoring singles for Houston.
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