"When you don't win, it becomes a burden for the team," Weligton said. "But the team is united and the result was fair considering the effort we put into it."
Villarreal went ahead in the 32nd when Bruno Soriano volleyed Ruben "Cani" Gracia's low cross into the far side of the net. But Malaga stifled the hosts' normally vibrant attack until its final push paid off.
Mexico forward Giovani dos Santos returned for Villarreal after missing the last two games with a muscle injury to his left leg. He showed his hasn't lost his speed when he raced to the end line and sent in a dangerous cross late.
Levante established the slow tempo that favored its defensive style in the first half that saw no clear chances from either side, leading to the sparse crowd at the Alonso Perez Coliseum jeering both sides as they walked off the pitch.
Levante threatened soon after the break but Getafe goalkeeper Miguel Moya saved Simao Mate's header in the 51st before Jordi Xumetra volleyed Papakouly Diop's lofted pass wide.
Getafe showed more verve in attack and broke through when Simao's attempt to clear the ball hit another player, with the ball falling for Leon to blast it in off the upright.
Getafe's win came six days after losing 7-0 to Atletico Madrid.
"We know that this wasn't our best game," said Leon. "But these are three important points after the big setback we suffered last week. Being Getafe, we are having a good season."
It was Levante's fourth straight loss and, depending on the round's other results to come, it could slip close to the drop zone.
On Saturday, Atletico and Real Madrid will try to put pressure on Barcelona with their respective games against Elche and Valladolid. Also, Real Sociedad visits Espanyol while Celta Vigo hosts Almeria.
Elsewhere on Sunday, it's: Real Betis vs. Rayo Vallecano, Granada vs. Sevilla, and Valencia vs. Osasuna.