In the 36th minute of the match, Mortlock contested a kick-off in which the Wallabies playmaker broke the third and fourth metacarpal in his right hand.
The 29-year-old has been plagued with injuries in the early part of the Super 14 season, having missed one game with a head knock and two more with neck soreness and a bruised jaw.
Brumbies coach Laurie Fisher was disappointed to lose his star player, and believed the result against the Cheetahs could have been different if not for the injury and some silly defensive mistakes.
"It certainly hurt us. We made some poor decisions defensively," Fisher said.
"I thought we'd done enough to be ahead but (two tries before half-time) rocked our confidence and gave was massive swing which gave them an enormous boost."
"At their home ground with the support of a home crowd, it was going to be challenge for us from there."
The match was evenly poised prior to Mortlock's departure but two late tries before half-time to Falie Oelschig and Gavin Passens gave the home side a 14-0 advantage at the break.
After half-time the Brumbies missed Mortlock's leadership and powerful presence with the Cheetahs slamming on a further four tries.