The Phillies seemed in command in the ninth behind Cliff Lee, who had tossed eight innings of shutout ball and held a 3-0 lead. But Carlos Quentin singled to lead off the frame and Chase Headley followed with a double, chasing the left-hander.
Phillies closer Jonathan Papelbon came in a promptly surrendered a two-run single to Blanks.
In the 10th, the Padres loaded the bases with one out against Justin De Fratus (2-1) and Blanks (4-for-5) then lined a hit over third base, chasing home Chris Denorfia with the winning run.
Joe Thatcher (3-1) got the decision for San Diego, which took the first of a three-game series.
Lee ending up allowing two runs on eight hits over eight full innings for Philadelphia, which began a 10-game road trip with a stunning loss.