A 15-yard penalty on the hit helped the Patriots to a touchdown.
At the start of the fourth quarter, the team announced Gronkowski would be out for the remainder of the game.
Gronkowski remained down on the turf as Church protested the call.
"I just tried to dislodge the ball", Church explained. If you go low for the knees you are considered a dirty player and if you go high, they throw the flag at you. It was a tough call, but you have to go with what they call.
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"It was definitely a momentum changer", Church said.
Gronkowski, who took the shot to the left side of his helmet, was dazed by the hit and came off the field.
"I think they were bad calls", he said.
"At the end of the day, they just made more plays than us", Fowler Jr. said.
The Patriots will play the victor of the NFC Championship Game in Super Bowl LII on February 4.