Toluca's defeat on Friday had given Tijuana the chance to go to the league summit and after a goalless first half Duvier Riascos gave the visitors the lead five minutes after the interval before Alfredo Moreno struck immediately after.
Esteban Paredes' strike for Atlante in the 87th minute ensured a nervy ending but Tijuana kept their composure to close out the game go two points clear of Toluca.
Angel Reyna's 75th-minute winner ensured Monterrey claimed a hard-fought 3-2 triumph at Puebla, who had battled back from two goals down.
Monterrey looked to be cruising when goals from Cesar Delgado and Aldo De Nigris gave them a comfortable cushion at half-time and although Diego De Buen and Isaac Romo scored to level proceedings, Reyna popped up to break Puebla hearts.
Luis Mendoza's strike 10 minutes after half-time helped San Luis edge out Unam Pumas 1-0 in Sunday's other clash.