The loss meant the holders were on the brink of elimination, giving a lifeline to UP Yoddha, who will face Bengal Warriors Thursday to decide the third team from Zone B.
Gujarat's defence proved to be the difference as they prevailed over Patna's star-studded attacking lineup featuring the season six's leading raider Pradip Narwal.
Captain Sunil Kumar, with five tackle points, was Gujarat's mainstay in the defence as he got a fine support from Iran's Asian Games gold medallist Hadi Oshtorak.
Leading by a slender three-point margin with three minutes left on the clock, the duo affected a super tackle to pin down Narwal to give them a decisive 32-28 point advantage.
Their defence grew stronger and stronger in the dying minutes as they scored five points in a row to seal their win and topped the group.
Narwal finished with 10 raid points but it was not enough with the Fortunegiants putting up a fine show in defence with their captain leading the way.
Already assured of the top spot in Zone A, Gujarat trailed most of the first half but they gained a slender one point lead at the break.
Gujarat scored some crucial raids through Ajay Kumar (8) and Rohit Gulia (10) to extend their lead by three points with less than 10 minutes.
Gujarat scored four points on the trot before effecting an all-out to make it 24-17 with less than 10 minutes left on the clock.
The Gujarat franchise trailed most of the first-half but in the last minute before the break they got a bonus point while their defence thwarted Manjeet's raid to take a slender 13-12 lead.
Season six's leading raider Narwal spearheaded Patna's attack as he made early inroads to give the defending champions a 6-2 lead.
Desperate for a win, Patna called a successful review to make it 12-9, with five minutes left for the break.
But the Fortunegiants, who are the most consistent team of the season, ensured that they kept Patna's lead in check with Gulia leading their attack.