Hunter was the intended receiver on a pass from DeShone Kizer. The ball hit Hunter in the hands, but Elliott landed a shoulder and helmet to Hunter's head and the ball fell incomplete.
A targeting foul was not called on the play though Notre Dame coaches called for one.
"It wasn't even reviewed, which makes no sense to me," coach Brian Kelly said after the game.
Hunter's father, retired Minnesota Twins outfielder Torii Hunter, took to Twitter and said his son is fine but has a concussion.
Hunter laid on his back for several minutes while Notre Dame training staff attended to him. He sat up, then walked off the field and was taken to the locker room. His father and other family members joined him.
The Irish also lost safety Avery Sebastian with an injury suffered during the second overtime of Sunday's 50-47 loss. After attempting to tackle Texas' Tyrone Swoopes, Sebastianwas inadvertently hit in the head by a teammate's leg.
Kelly said Sebastian's injury seemed like a shoulder injury or stinger.
Information from The Associated Press was used in this report.