Howard, 32, had spent the entire season on the disabled list following offseason surgery on his left Achilles.
He played in a combined seven rehabilitation games for Lehigh Valley and single-A Lakewood and batted .500 (10-20) with two doubles, one home run, 10 RBI and five walks.
Howard also appeared in several extended spring training games prior to beginning his official minor league rehab assignment.
To make room for him on the 25-man roster, the club optioned infielder Hector Luna to triple-A Lehigh Valley.
Luna, 32, appeared in 26 games for the Phillies this season and hit .246 with two doubles, two home runs and 10 RBI. After not playing in the major leagues last year, he hit a pinch-hit grand slam in his first at-bat of the season at Wrigley Field on May 16.