Philadelphia (5-10-3) snapped a two-game losing streak and Seattle (9-6-2) lost its second straight.
Sapong headed in Sheanon Williams' perfectly chipped cross in the 69th minute.
Philadelphia had a goal waved off in the 27th minute after Andrew Wenger fouled goalkeeper Stefan Frei on a long throw in. In the 30th, Wenger was fouled in the penalty area on a high kick. Maurice Edu's penalty kick was blocked and gathered by Frei.
Seattle struggled in the attacking half, playing without injured Obafemi Martins and suspended Clint Dempsey. Marco Pappa's shot from distance in the 83rd minute was Seattle's first attempt on target. The Sounders did not have a corner kick until the 87th.
The Sounders will face rival Portland on Sunday for their third game in eight days.