Much of his ire was directed at a disputed non-call on the Utes' final offensive play of the game.
With less than a minute left, Huskies cornerback Byron Murphy appeared to run into Utah wide receiver Siaosi Mariner prematurely while breaking up a pass on fourth-and-12 from the Washington 42. But officials didn't throw a flag, and the Huskies burned off the rest of the clock to clinch their first Rose Bowl berth in 17 years.
Whittingham could be seen yelling at officials as he made his way off the field in the game's waning seconds. He was still fuming almost a half-hour later during his postgame news conference.
"I don't know what I can say," Whittingham said. "Wouldn't you be upset? I'm used to it."
It was the latest controversy over how the Pac-12 has handled officiating, an enduring story this season following a recent Yahoo report that the league's general counsel overruled a call in the Washington State-USC game in September. Pac-12 commissioner Larry Scott was later forced to acknowledge the error in the system and make a short-term change in protocol.
In a pregame news conference Friday, Scott said of the WSU-USC incident: "Our athletics directors were all satisfied that this was an isolated incident, and any other call in the game was not affected by the one call in question."
During the postgame trophy presentation, Scott was repeatedly booed. He could barely be heard in the stadium as he attempted to present the MVP trophy to Murphy, who finished the night with two interceptions, including one he returned for the game's only touchdown in the third quarter.
"I'm just glad he didn't get caught," Washington coach Chris Petersen said. "When I saw him cut back, I was like, 'please keep going.'"
Huskies fans only stopped heckling Scott when Murphy made his way to the microphone on the stage hastily set on the field. But it quickly restarted when Scott spoke again to present the league's championship trophy to Petersen.
It was easily one of the loudest moments of the night at Levi's Stadium, where an announced crowd of 35,134 -- the second-lowest in the eight years of the game's existence -- didn't have much to make noise about until the final minutes.
Washington (10-3, 7-2 Pac-12) barely held off the Utes (9-4, 6-3) in the championship game, vindicating its status as the league's preseason favorite but in a deeply unsatisfying fashion. The Pac-12 will be shut out of the College Football Playoff for the third time in four years, confirming its status as the weakest of the Power 5 conferences.