The record 11-times league champion Chivas are nine points adrift of joint leaders Tigres UANL and Apertura champions Tijuana in 14th place with four points.
For the second match in a row, Guadalajara took the lead but conceded an equaliser as they struggle to rebuild after the failed experiment with Dutch great Johan Cruyff's consultancy last year.
Mexico forward Marco Fabian gave the Chivas the lead in the first half of the home match at the Omnilife.
Argentine striker Mauro Matos put San Luis, who now have two points, level in the 55th minute with shot inside the box from a long throw-in.
The top of the table clash in Monterrey between Tijuana and Tigres ended in a 2-2 draw on Saturday.
With America also beating Queretaro 3-0 on Saturday, the leaders' advantage was cut to one point. Unbeaten Tijuana and Tigres have 13 points from five matches to America's 12.
America's 21-year-old striker Raul Jimenez, a member of Mexico's 2012 Olympic gold medal team, scored twice with Ecuador's Cristian Benitez adding a late penalty.
"Raul is in sensational form ... We gave him his chance and he's responded like a proper centre forward, with goals, attitude and determination," Eagles coach Miguel Herrera told reporters.
Atlas, who won 2-1 at Chiapas, are fourth while Cruz Azul are fifth after claiming a 2-2 draw at Leon thanks to a brace from their Argentine striker Mariano Pavone.