"Our goal is to win a Pac-12 championship. I know a lot of people still laugh about it, but that's what those young men believe and if we can't believe it than we can never achieve it," he said.
Colorado (3-1) had not been able to defeat the Ducks since joining the Pac-12 in 2011 until Saturday, when Steven Montez threw for 333 yards and three touchdowns in a 41-38 victory.
Ahkello Witherspoon intercepted Dakota Prukop's pass to Darren Carrington in the end zone on Oregon's final drive to preserve the win.
Afterward MacIntyre hugged his son Jay, a sophomore receiver, and wiped away tears as the team celebrated.
The Ducks were stunned.
"I haven't been through something like this before. It sucks," Prukop said. "You've just got to eat it, learn from it. Can't let it happen again. Just move on."
The Buffaloes had retaken the lead following a controversial 31-yard touchdown from Montez to Bryce Bobo. After review, the officials ruled Bobo had control of the ball in his right hand when his right foot came down in the end zone — but the crowd at Autzen Stadium booed in disagreement.
"I'm never confident on anything that goes to review, and I don't mean that negatively. You just don't know," MacIntyre said. "But the way he caught it and his was foot was in, I thought they'd give it to him. You could see he had possession and he didn't bobble it."
The Buffaloes led from the start and went up 33-17 following Montez's 48-yard TD pass to Devin Ross to open the second half.
But Kani Benoit scored on a 3-yard touchdown to pull Oregon (2-2) within 33-31. Troy Dye's interception on Colorado's subsequent possession led to Prukup's 18-yard go-ahead TD pass to Carrington late in the third quarter.
The Buffaloes led 21-7 against Michigan last weekend but fell behind to lose 45-28. Oregon was coming off a 35-32 loss at Nebraska last weekend.
Both teams were without key playmakers.
Oregon running back Royce Freeman, who left the game against the Huskers after five carries with a leg injury, watched from sidelines although he warmed up in pads with the team. Kani Benoit made his first career start in Freeman's place.
The Buffaloes didn't have senior quarterback Sefo Liufau, who left the game at the Big House with an ankle injury after throwing for 246 yards and three touchdowns.
Montez, who also rushed for 135 yards, was the first Colorado quarterback ever to throw for more than 300 yards and rush for more than 100 in a single game.
"I sensed the momentum change but I knew it wasn't going to slip away because we are a different Colorado team. We're mentally tough, we're mentally strong and we're confident," Montez said. "I knew the game wasn't going to slip out of our hands."