Uruguayan Ruben Israel, meanwhile, became the first coach to lose his job this year, sacked by Atlante after they lost 2-1 at Veracruz on Saturday.
The 23-year-old holding midfielder stormed into attack to open the scoring after three minutes in Saturday's match at the Estadio Leon.
Pena saw Atlas goalkeeper Federico Vilar advancing towards him and beat the Argentine with a fine lob.
"You have to study goalkeepers. I knew Vilar, who is a great keeper, likes to come out into his box," Pena told Fox Sports.
"I'm improving my finishing, my attacking team mates have given me plenty of advice and I'm getting better."
Pena, who made his international debut during the World Cup qualifiers in 2012, scored again before halftime, breaking through after a pass from Luis Montes and rounding Vilar to slot home.
Montes added Leon's third with a shot from outside the box into the top corner in the 77th and Brazilian Maikon pulled one back two minutes later.
The win gives the champions, winners of the Apertura in the first half of the season, four points from two matches.
Atlante, who finished the Apertura one from bottom, had drawn their opening Clausura match 1-1 at home to Leon last weekend.
"After a deep analysis by the Atlas board and the unfortunate lack of results, coach Ruben Israel leaves the team's reins," Atlante said in a statement.
Queretaro were the only team with a maximum six points after a 1-0 home win over UNAM Pumas on Friday and before Toluca's match at home to Morelia on Sunday.
America's Argentine coach Antonio Mohamed made a losing return to Tijuana on Friday when his "Eagles" side lost 1-0 to the border town team he steered to the 2012 Apertura title.