The 19-year-old Aspar rider, who was also on pole at Aragon earlier this year, joined forces with Miguel Oliveira's Monlau Suter-Honda for a final flying effort as the chequered flag flew.
Both men helped spur the other on, duly capturing first and second respectively at the death.
Their late improvements denied Luis Salom a maiden pole, the 21-year-old having jumped more than three tenths of a second clear with six minutes of the session to run.
Folger and Oliveira also pushed 2012 champion Sandro Cortese down to fourth, the first time since Silverstone in June that the Ajo KTM rider has not started on the front row.
He will line up alongside his once-title rival Maverick Vinales and Efren Vazquez.
Vinales had set the pace for much of the session, threatening to capture his sixth pole of the year and his first since his acrimonious spat with his Avintia team.
He was unable to get out in the crucial final 10 minutes however, and was therefore helpless to respond as he was gradually bumped down to fifth.
Danny Kent, Niccolo Antonelli and Luis Rossi completed the third row, with Rossi just shy of eight tenths slower than Folger.