The Buffaloes (1-4, 0-1) were primed for a win in their Pac-12 debut before surrendering two touchdowns in the final 2 1/2 minutes. Colorado had thwarted Washington State's high-powered aerial attack most of the afternoon with a patchwork secondary that included two converted offensive players.
Lobbestael threw for 376 yards and three touchdowns in leading the Cougars (3-1, 1-0) to just their second road win in four years under coach Paul Wulff.
The Buffaloes led 27-17 with 5:11 left after Rodney Stewart's 1-yard TD run, which he set up with a 52-yard scamper to the Washington State 21.
Lobbestael led Washington State 77 yards in seven plays, hitting Isiah Barton from 19 yards out with 2:35 left to pull the Cougars within a field goal.
With three timeouts remaining, Wulff elected to forgo a risky onside kick, and the strategy paid off when the Cougars forced a punt and got the ball back with 1:50 left.
This time, they needed just 40 seconds to cover 90 yards.
Bottled up for much of the afternoon -- 58 yards on five catches -- Wilson sped past cornerback Greg Henderson and safety Anthony Perkins and was wide open as he hauled in the pass and raced into the end zone.
The Buffs had one more chance, but receiver Paul Richardson was stripped of the ball by cornerback Damante Horton after a 23-yard gain and linebacker C.J. Mizell recovered for Washington State at its 39 with just under a minute left.
Afterward, Buffaloes coach Jon Embree declared he was tired of losing and ripped into his team for finding a way to lose another winnable game.
Until the final few minutes, it looked like the Buffs were going to win despite a rash of injuries that has sidelined six cornerbacks -- a seventh missed the game while tending to a family matter -- forcing converted wide receiver Jason Espinoza and converted tailback Brian Lockridge to line up as defensive backs when the Cougars went with multiple-receiver sets.
Espinoza had a quarterback hurry that forced a punt, and Lockridge, who had never played defense before Monday, had five tackles and a sack.
Tyler Hansen threw touchdown passes of 9 yards to Richardson and 4 yards to Toney Clemons, the latter giving Colorado a 20-10 lead in the third quarter. Lobbestael responded with an 11-yard TD strike to fullback Jared Byers to keep it close.
Will Oliver's third field goal, a 48-yarder as the first half expired, gave Colorado a 13-10 halftime lead. It came just 16 seconds after Andrew Furney tied the game with a 28-yarder following Hansen's first interception in 133 passes.