Baptista, who is known as the 'Beast', hovered in the air over the penalty spot in stoppage-time and lashed his shot into the top corner to leave the big-spending south-coast club on 13 points from six games, ahead of Valencia on goal difference.
A goal from Sergio Canales earned Valencia a 1-0 home win over promoted Granada earlier in the day.
Dutch striker Ruud van Nistelrooy scored his first goal for Malaga with a back-post header but again Getafe went in front, the ball appearing to go in off substitute Miku's arm in the 75th minute.
"It's my 30th birthday, I´ve just become a father to a daughter two days ago, it's all coming at once," Baptista told Spanish television.
"We are top of the table, we'll have to see where it goes from here."
Well-worked goals from Zaragoza's Luis Garcia and Pablo Barrera in the first half had Villarreal on the back foot despite Giuseppe Rossi briefly levelling at 1-1 with a twice-taken penalty in the 41st minute.
A red card for Zaragoza's Maurizio Lanzaro lifted the hosts and Hernan Perez headed in from a corner on 84 minutes.
"The public have the right to give their opinion and I respect it," said coach Juan Carlos Garrido when asked about criticism from the fans.
"All I can do is continue working with humility and enthusiasm to try and change this situation."
Mallorca's 2-2 draw at Osasuna was played against a background of boardroom squabbles after the visitors parted company with coach Michael Laudrup in acrimonious ci
