Le Toux's first goal of the season came after San Jose's Jason Hernandez was whistled for a hand ball inside the goal crease.
Philadelphia played a man down for the final 49 minutes after defender Jordan Harvey was issued a red card and ejected for violent conduct against San Jose's Chris Leitch just inside the midfield.
Union goalkeeper Faryd Mondragon picked up his fourth shutout in helping Philadelphia improve to 4-1-1 and jump back into first place in the Eastern Conference with 13 points.
San Jose fell to 1-4-2 and remains in last place in the nine-team Western Conference.
