The Rays won their fifth in a row overall.
Roberto Hernandez (2-4) pitched six innings, giving up five hits and two runs.
Fernando Rodney pitched the ninth inning for his 11th save.
The Rays trailed 2-1 in the sixth when Evan Longoria, who hit a winning two-run homer with two outs in the ninth Saturday night, led off with a double. Rodriguez hit a tying single off Eric Stults (3-3), moved up on a wild pitch by Brad Brach and scored on Escobar's double for a 3-2 lead.
Loney, hitting .456 in his last 24 games, connected for his third homer of the season in the eighth off Dale Thayer.
Longoria scored twice. He walked in the second and headed home on a bases-loaded sacrifice fly by Jose Molina.
Stults pitched 5 1-3 innings, giving up three runs on five hits and five walks.
NOTES: RHP Burch Smith, who pitched only 1 1-3 innings for the Padres in his major league debut Saturday night, will start at home next weekend against Washington. Manager Bud Black said he plans to use "the same rotation for the foreseeable future." ... Rays CF Desmond Jennings was out of the lineup for a third straight day. The Rays have acknowledged no injury for Jennings, who is on a seven-game hitting streak. . . Amarista's home run was the Padres' 19th in 14 games. They hit only 12 in their first 23 games.