Guerrero nailed a 3-pointer from the right wing with 32 seconds left and Jones finished a layup with five seconds remaining as Fresno State beat Air Force for the sixth straight time.
Zach Kocur answered Guerrero's trey with his own 3 with 21 seconds left to give the Falcons a 55-54 lead. Julien Lewis missed a jumper on the other end but Jones grabbed the rebound and put it back for the win.
The last three games between the two schools have been decided by two points or less, with Fresno State winning all three.
Jones and Marvelle Harris had 14 apiece for Fresno State (13-7, 4-3 Mountain West). Guerrero finished with 10.
Trevor Lyons had 12 points to lead the Falcons (10-10, 1-6).