Lenhart and Wondolowski had a goal in each half, giving the Earthquakes their seventh win in nine games this year. San Jose leads MLS with 22 points.
San Jose owned a 3-1 lead at halftime, but Daniel Woolard brought United with a goal in the 64th minute.
Wondolowski tallied 5 minutes later and Lenhart's second goal came soon after to wrap up the victory.
D.C. United (4-3-3), in second place in the Eastern Conference), had a six-match unbeaten streak come to an end.