And rightfully so, because there were some questionable calls, or lack thereof, between the Baltimore Ravens and the 49ers.
Factor in a second-half delay that was basically an extended halftime, and that only enhanced Harbaugh's agony.
Here, we look at some of his best antics through his career.
Super Bowl XLVII
(GIF Credit: Stephen Douglas, The Big Lead)
Harbaugh first shuffles to his left then throws his arms up and back down in what looked like Chris Farley playing Matt Foley.
The pen, headset and play-sheet went everywhere and he was left breathing heavily.
Where's a coffee table to fall on when you need one?
NFC Championship Game Against the Atlanta Falcons
The sideline theatrics continue here after a call during the NFC title game goes against the 49ers.
Harbaugh hits the ground, everything goes everywhere and his arms become uncontrollable. It's quite a sight to see.
2011-12 Season vs. Jim Schwartz
During the 2011-12 season, Harbaugh barely shook hands with Jim Schwartz, the Detroit Lions head coach. Immediately after, Harbaugh and Schwartz got into it and the incident escalated from there.
The aftermath was so intense each team entered the locker rooms separately.
Versus Pete Carroll in College
Revert back to his college days at Stanford, where Harbaugh got into a minute exchange of words with Pete Carroll. Carroll was the head coach at USC during this meeting, and ironically, the two square off twice per season in pro football.
Therefore, as time progresses, expect the 49ers-Seahawks rivalry to only get more intense between these coaches.
Week 1 at Green Bay in 2012-13
Opening kickoff of the 2012-13 season, and Harbaugh goes rabid in the first quarter. Then again, San Francisco is playing on the road against Aaron Rodgers and the Green Bay Packers.
For a Week 1 matchup in the NFC, it's quite a colossal showdown. And this is the Harbaugh who is happy. We can only imagine Harbaugh when angered.
Aside from becoming hungry for Thanksgiving, does anyone have any idea what Harbaugh is talking about here? Clearly, mass hysteria set in and he briefly lost his mind, but it's entertaining nonetheless.
Back at Stanford, Getting Pumped Up
For anyone who has ever played football, having a coach of Harbaugh's passion is a plus. They get you fired up before the game and focused to knock the snot out of someone. After all, the physical aspect of football is the most appealing.
Playoff Game vs. Green Bay
Harbaugh mixes it up this time by stomping his feet. Perhaps river-dancing or tap-dancing would be a good hobby. And we also see his emotions once again, because the game brings it out of us all.