Idaho took its first lead of the game when Justin Veltung scored off a 37-yard run with 14:50 left in the fourth quarter to give the Vandals a 17-13 lead.
Trey Farquhar added a 32-yard field goal with 7:14 to go, giving Idaho a 20-13 lead.
SJSU's Ryan Otten snagged a 6-yard pass from La Secla with 4:35 left to tie the game at 20.
The Spartans put up 496 yards of offense to Idaho's 421, but Waid proved to be the difference. He missed an extra point attempt in the third quarter could have won the game in regulation if his attempted wasn't blocked.