Martin has seemed powerless to stop two-time defending champion Bagnaia eating into his once sizeable championship lead as the Italian has won the last three races.
The 27-year-old Italian trails by just 10 points and could emerge from the weekend at the top of the standings.
However, Martin seemed unaffected by the pressure as he set a new lap record in qualifying on his Ducati-Pramac.
The 26-year-old erased the mark set by compatriot Maverick Vinales on Friday. Vinales had a less happy experience on Saturday being taken to the medical centre after crashing but was later given the all-clear to ride.
The two Aprilia-Trackhouse riders Miguel Oliveira of Portugal and Spaniard Raul Fernandez will start alongside Martin on the front row.
Bagnaia lurks on the second row having posted the fourth fastest time on his factory Ducati bike.
"I was not expecting to finish on pole," said Martin.
"My lap really was not fantastic.
"However, all round I feel competitive and very powerful, though the Aprilia's also appear to be."
Martin is certainly in a better place than his legendary compatriot six-time MotoGP champion Marc Marquez, who is third in the title race but starts from 13th spot.
He may have been hindered by a broken left index finger and a bruised ribcage which he suffered in a crash on Friday but was declared fit to compete.
Marquez would have eyed the race as one where he could make ground on Martin and Bagnaia as he has flourished on the Sachsenring track, winning a record eight German MotoGPs.
