Scans immediately after the match indicated the flanker had suffered ligament damage, although the full extent of the injury will not be known until he returns to Sydney next week.
"I got up and tried to run and it felt like the ankle gave away a little bit," said Waugh. "It certainly wasn't good but we'll just have to wait to see how it comes up over the next few days."
Depending on the extent of the damage, Waugh could face up to six months on the injury list, casting doubts over his preparations for the World Cup later this year.
Wallaby team-mate Stephen Moore is also facing an extended spell on the sidelines after an injury at the weekend.
The Queensland Reds hooker will undergo arthroscopic surgery next week after he tore the meniscus in his left knee in the 6-3 loss to the Brumbies on Saturday.
Moore came off the bench before the interval to replace Sean Hardman, but was carried off the field midway through the second half and is now facing at least one month out of action.
"Depending on the seriousness of the tear he could miss between four weeks and four months," said Reds coach Eddie Jones.
Jones has further injury doubts over winger Peter Hynes, who sprained an ankle on Saturday and is rated 50-50 to face the Blues in Auckland next weekend.
And Reds centre Lloyd Johansson has also been suspended for two matches following a judiciary hearing on Sunday for his high tackle on Stirling Mortlock late in the match against the Brumbies.