The visitors moved out of the Primera Division relegation zone on goal difference as they punished their opponents for twice handballing in the area.
Siqueira's first spot-kick cancelled out Juan Rodriguez's opener, but the hosts were back in front shortly before the break thanks to Paco Alcacer.
And they looked set for a win before Siqueira made the most of his second opportunity from the spot two minutes into added time.
The draw took Granada above Real Mallorca on goal difference as Getafe stayed in 11th place.
The hosts went in front in the 18th minute when Adrian Colunga swung in a free-kick from the left and Rodriguez got to the ball ahead of goalkeeper Roberto Fernandez and stabbed it inside the near post with his knee.
Colunga had a close-range effort saved, while Fernandez fumbled a Juan Valera shot from range as Getafe threatened a second.
But they were undone in the 27th minute when David Abraham was penalised for handball in the area and Siqueira coolly dispatched the resulting penalty into the left corner.
Getafe went back in front three minutes before the break, with Colunga again the architect.
His pass set up Alcacer to dink a shot into the right corner from inside the area.
Granada started the second half brightly with Yacine Brahimi and Mikel Rico Moreno trying their luck from distance before Siqueira shot over from inside the area.
An even better chance came in the 69th minute when Odion Ighalo's shot from six yards was parried away by Miguel Moya.
They left gaps at the back, though, and their opponents threatened a third.
Colunga had a shot saved by the feet of Fernandez before firing the follow-up against a post, while five minutes later the keeper produced a brilliant save to deny Pablo Sarabia from close in.
But Getafe conceded another penalty in stoppage time when a controversial handball was given against Rafael Lopez and Siqueira converted his second spot-kick of the night, going the same way as earlier, to earn Granada a point.