The 2011 Apertura champions have taken 28 points from 12 matches with Atlas, who beat Cruz Azul 2-1 away on Saturday, in second place.
Tigres went ahead after half an hour when Argentine Lucas Lobos found fellow midfielder Juninho on the right and the Brazilian volleyed the ball into the middle to set up Spaniard Luis Garcia for the score.
Former U.S. international DaMarcus Beasley, a second half substitute, put Puebla back on level terms in the 58th minute when he rose between the central defenders to head home the equaliser from a William Paredes cross.
Tigres, who hit the post though Garcia three minutes later, scored the winner in the 86th minute when Alan Pulido tapped in after Puebla goalkeeper Hugo Hernandez had failed to hold a stinging shot from substitute Elias Hernandez.
Champions Tijuana, winners of the Apertura title in the first half of the season, lost 1-0 at Toluca on Saturday, their fifth defeat in the championship.
Tijuana, who have concentrated this year on their debut participation in South America's elite club tournament the Libertadores Cup, dropped out of the top eight in the standings.
After the 17 rounds of the league format, the top eight qualify for the knockout phase.