Wagner began in 1996, once again in the minor leagues as a starting pitcher, but he finished the season by becoming a relief pitcher for the Astros. He accumulated a 6–2 record with a 3.28 ERA, in twelve starts for the AAA Tucson Toros. His baseball contract was purchased by the Astros on June 2, 1996, and Wagner was then assigned exclusively as a short-relief pitcher by the Astros manager. He finished the Major League season with nine saves in 13 opportunities, allowed 28 hits, and he struck out 67 hitters in innings – giving him a rate of 11.7 strikeouts per nine innings pitched. His opponents had a batting average of .165 against him.