Dante Lopez's goal two minutes from the end handed Pumas UNAM a 1-0 win on Saturday and condemned America to their first defeat in seven rounds.
That loss saw rivals Monterrey (+6) join America (+8) on 16 points, but behind on goal difference, after edging Queretaro 1-0 on Friday.
America went into their home fixture against strugglers Pumas UNAM at the Estadio Azteca with a run of back-to-back draws in all competitions, though they had won six successive games prior.
Antonio Mohamed's America were forced to play out a goalless stalemate at Chiapas in their most recent league match, while a midweek CONCACAF Champions League trip to Comunicaciones saw them held to a 1-1 draw.
And America were seemingly on track for yet another draw, until Paraguayan attacker Lopez found the back of the net from outside the box in the 88th minute, albeit after the ball took a deflection and looped over goalkeeper Moises Munoz.
Former Chile international striker Humberto Suazo was the hero for Monterrey, who beat Queretaro a day earlier.
Suazo's close-range effort three minutes before the half-time break proved the difference at the Estadio La Corregidora.
Monterrey have now won three games on the bounce.
Atlas' stuttering form continued after they drew 1-1 at home to Santos Laguna on Saturday.
In a match pitting third versus fourth, Santos Laguna took a 39th-minute lead thanks to Javier Orozco.
Atlas hit back on the hour-mark, when Edy Brambila found the back of the net.
Both teams finished the match with 10 men following second yellow cards to Luis Venegas (Atlas) and Alberto Lozoya (Santos Laguna).
In other results, Hirving Lozano scored a first-half brace as fifth-placed Pachuca prevailed 2-1 over defending champions Leon, who slumped to back-to-back losses.
Leon's Juan Gonzalez saw red in the 33rd minute, while Pachuca's Jorge Hernandez was dismissed in the final moments.
A brace from Wilberto Cosme inspired Puebla to a 3-2 victory against winless Morelia, who are bottom of the table.
Elsewhere, Chiapas saw off Tigres UANL 2-0.
Tijuana and second-bottom Universidad Guadalajara played out a 1-1 draw.
Veracruz lost 2-1 at Toluca, while Guadalajara held Cruz Azul to a scoreless stalemate.