Real Salt Lake became the first team to play all of its regular season games, and put itself in position for an unlikely Shield win.
Real Salt Lake took a 1-0 lead shortly after the start of the second half. Chivas USA defender Mario de Luna was judged to have played the ball in the box with his arm, and Alvaro Saborio was true from the spot.
The Royals doubled up in quick succession. Javier Morales was dispossessed at the top of the area by de Luna, but the ball fell to Joao Plata, who struck from range to beat Tim Melia and make it 2-0 in the 52nd minute.
Chivas USA responded with a goal from Julio Morales in the 77th minute. Morales - seconds after entering the game as a sub - beat the offside trap and got in behind the unaware Tony Beltran to beat the oncoming Nick Romando with a deft touch.
Salt Lake (16-10-8) takes top spot both in the Western Conference and MLS, but could fall after the league's final regular-season matchday this weekend, with Portland close behind in the conference standings and New York and Kansas City challenging for national dominance.
Chivas USA (6-19-8) will end its season at home to Portland on Saturday.