Di Giannantonio's record-setting time of two minutes 0.136 seconds secured back-to-back pole positions for the Italian who topped qualifying in Brazil last weekend.
MotoGP championship leader Marco Bezzecchi qualified second fastest for Aprilia, with KTM's Pedro Acosta completing the front row.
"The team did an incredible job yesterday because we did a big change for this morning and they sent perfectly what they needed to improve, to be faster. For this, I'm super grateful to them," Di Giannantonio said.
"Then we did an amazing lap. This lap was the most adrenaline-packed lap of my life, honestly.
"For sure, it's a great shot to start from where we are. But we need to be focused and try to give our best in the afternoon (sprint)."
Lap records tumble
Saturday's qualifying turned into a record-breaking bonanza, with the lap record changing hands multiple times during the session.
Ducati's former world champion Francesco Bagnaia set the early pace in Q2 by breaking the track record.
But his moment in the spotlight lasted barely two minutes until Joan Mir stunned the field by shattering the record again aboard his Honda.
Ducati's reigning champion Marc Marquez was repeatedly frustrated by traffic as he attempted to set a fast lap while his Ducati teammate Bagnaia was seen slapping his fuel tank when other riders impeded his bid for another quick time.
Stewards said they were investigating an incident in which Bezzecchi cut across Marquez, forcing the Spaniard to slow down and abandon his flying lap.
"Honestly, I have no idea. I didn't see him," Bezzecchi said when asked about the incident.
Despite the qualifying chaos, Bagnaia managed to secure fourth position on the grid, relegating Mir to fifth. Marquez will start sixth in Sunday's race after setting a time that was half a second slower than Di Giannantonio's pole-winning effort.
Aprilia's Jorge Martin was seventh fastest and is joined on the third row by Gresini Racing's Alex Marquez and Honda's Luca Marini.