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.
The Spanish youth international, on loan from Real Madrid, scored from outside the area in the fourth minute but Valencia lived dangerously before securing victory.
Another Real loan player, Pedro Leon, fired Getafe ahead against Malaga, controlling the ball on his thigh before volleying in from outside the area after 55 minutes.
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.
Getafe had Mehdi Lacen sent off as tempers flared in the aftermath of the disputed goal and Malaga came roaring back.
Enzo Maresca bundled in an equaliser with two minutes remaining before Baptista brought the Rosaleda to its feet at the end.
"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."
TROUBLED TRIO
The troubled trio of Villarreal, Real Mallorca and Racing Santander all rallied to grab draws on Saturday.
Villarreal were held at home 2-2 by Real Zaragoza, their late equaliser coming only after the visitors had been reduced to 10 men.
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.
Villarreal have now managed only one win from their last eight outings in all competitions.
"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
