Gwynn's line drive to right off Pat Neshek scored Juan Uribe, who had led off the 11th with a double against Ernesto Frieri (0-1), and Neshek's wild pitch allowed another Dodgers run to come home.
Jonathan Broxton notched his fourth save with a scoreless bottom of the 11th for the Dodgers.
The Dodgers and Padres endured four rain delays for a total of 3 hours and 36 minutes Friday night before the 2-2 tie game was finally suspended just before 2 a.m.
Blake Hawksworth (1-0) picked up the victory with two scoreless innings of relief and Matt Kemp finished 3-for-4 with an RBI for Los Angeles.
Orlando Hudson went 2-for-4 with a run scored and an RBI for the Padres.