Last week's 3-0 home defeat to the Texas outfit brought an end to a four-match unbeaten streak - three wins, one draw - which saw Columbus make a beeline into the top four of the Eastern Conference.
However, Gregg Berhalter's side looked determined to get that result out of their system as they stunned the hosts with a quick-fire double today.
First, Kei Kamara headed home after Harrison Afful's cross was flicked into his path by opposition defender Steven Vitoria, before the striker completed his brace on 26 minutes by sliding home Afful's teasing ball.
The hosts continued to exert pressure and it eventually paid off when Sapong tapped home Sebastien Le Toux's cross from close range on 66 minutes to throw the Union a lifeline.
Reducing the deficit served to reinvigorate Philadelphia, who looked certain to equalise 12 minutes later, but Clark reproduced his heroics by tipping Le Toux's effort against the crossbar.
It proved as close as they came to drawing level as Columbus dug deep to earn the hard-fought three points.