Gwynn, who passed away on June 16 after a battle with cancer of the salivary gland, played all 20 years and 2,440 games of his Major League career with the Padres.
That career started against the Phillies at Jack Murphy Stadium in Mission Valley, the Padres' home at the time.
Gwynn, hitting fifth and playing center field, went 2-for-4 with a run scored and an RBI.
He had to wait until the eighth inning for his first hit, a double off Sid Monge. He added a single in the ninth inning against Ron Reed, but the Padres fell, 7-6, before a crowd of 33,558.
Those two hits were the first of many for Gwynn, who finished with 3,141. He went into the Hall of Fame in 2007.
On June 27, a crowd of 23,229 gathered at Petco Park for a memorial tribute to Gwynn, a moving tribute that included speeches by Reggie Jackson, Trevor Hoffman and Gwynn's agent and longtime friend, John Boggs.