At the end of the game MacIntyre chased the officiating crew off the field screaming at them, before being flanked by police and security and herded back to the field. In a statement, Pac-12 commissioner Larry Scott called MacIntyre's conduct "completely unacceptable."
"Such misconduct violates conference policy and this behavior will not be tolerated," Scott said.
A critical interception for Colorado was called off in the second half because of a pass interference penalty. MacIntyre told reporters after the game "it was a huge momentum-changer," but would not comment on the officiating or his postgame tirade.
"The conference assigns a high priority for administrators, coaches and student-athletes to support its officiating program," Scott said. "Chasing and confronting an official or officiating crew after the contest fails to meet these high standards."
Proceeds from the fine will go toward the Pac-12 student-athlete scholarship fund.
Colorado (2-4, 0-3 Pac-12) has a bye this week before traveling to USC on Oct. 18.