Antonio Mohamed's America sit top with 17 points but have now failed to win any of their last three Apertura games as they were held to a 0-0 draw by struggling Universidad Guadalajara.
America remain at the table's summit in part because of the suspension of Monterrey's clash with Chivas Guadalajara.
Second-placed Monterrey could have leapt above America with a win at Estadio Tecnologico, but treacherous weather forced authorities to call off Saturday's contest.
Nevertheless, America had been expected by most to cruise back to winning ways following a defeat to Pumas UNAM and a draw at Chiapas.
But they failed to live up to expectations and Mohamed blasted his side's performance as their worst display of the season.
The match also saw America extend their goalless run to 265 minutes and Santos were the main beneficiaries of their disappointment, closing to within two points of the pacesetters.
Following Mauro Cejas' 10th-minute opener, Leon's task was made even tougher as Fernando Navarro received his second yellow card just before the half-hour mark.
Jose Maria Cardenas followed his team-mate's example 14 minutes from the end as he also saw red, and Jesus Escoboza wrapped up the win late on, squeezing a controlled effort past Christian Martinez in the visitors' goal.
Atlas would have gone level with America on 17 points with a win at Veracruz on Saturday.
However, Luis Caballero's 47th-minute goal was only enough to secure a draw, cancelling out Carlos Ochoa's first-half opener.
Queretaro had grabbed the headlines in the build-up to their meeting with Puebla on Saturday, following on from their signing for former Ballon d'Or and World Cup winner Ronaldinho.
The Brazilian was not able to make his debut, but supporters were treated to dramatic scenes nonetheless, with Camilo Sanvezzo putting the hosts ahead in the 89th minute, despite Miguel Angel Martinez receiving harsh red just after half-time.
Mexico legend Cuauhtemoc Blanco played a role in Martinez's sending off and the 41-year-old netted Puebla's equaliser in the seventh minute of stoppage time, smashing home a penalty.
Cruz Azul's unimpressive Apertura form continued as they were beaten 2-1 at home by Toluca, with the hosts having goalkeeper Jose Corona sent off at the death.
Elsewhere, Tijuana drew 1-1 at Pachuca, rock-bottom Morelia picked up a point at Chiapas, and Tigres UANL came from two goals down to draw 2-2 at Pumas.
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