Halliday (3-1) allowed only one run and scattered five hits and a walk in a dominating, 130-pitch performance as the Phillies won their 11th straight game at Petco Park and swept a four-game series against the Padres.
Antonio Bastardo picked up his first save after Will Venable reached Halliday for a run-scoring single with two outs in the ninth.
Shane Victorino homered and Ben Francisco contributed two hits and an RBI for the Phillies.
Padres starter Wade LeBlanc (0-1) surrendered three runs on nine hits and four walks over eight innings. He struck out two.