The expansion Union (3-7-1) posted a win while celebrating the first game in their new soccer-specific stadium, PPL Park, with a crowd of nearly 19,000 watching.
Fred gave Philadelphia the lead in the 79th minute with his first goal of the year after Le Toux's shot found him at the back post for an easy tap-in.
Mwanga notched an insurance goal on another penalty kick in the 84th minute.
Seattle (4-7-3) got its goal from Pat Noonan 44 minutes into the contest.
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