Wallabies captain Stirling Mortlock has been cleared of a serious leg injury after a sickening collision during the Brumbies' 25-17 Super 14 loss to the Lions in Johannesburg.

Mortlock hobbled off Ellis Park in the second half after his leg was bent back awkwardly, but early indications are he suffered only a cork and could be available for the clash with the Sharks on Saturday (Sunday AEDT).

"At this stage it appears that Stirling has suffered a corked thigh in both legs," Brumbies doctor Warren McDonald said.

"We will monitor him over the next 48 hours and see how he pulls up."

Mortlock walked freely on Sunday and will not require scans, a Brumbies spokesman said.

Coach Andy Friend lamented his side's inability to finish off the South African strugglers, who rebounded from a racism row to post their first victory over the Brumbies since 2003.

The Canberra side hit the front soon after halftime but Lions fullback Louis Ludik sealed the three-tries-to-two win with a final-minute try after a Brumbies mistake deep in their own territory.

The loss meant the Brumbies slipped to ninth on the ladder, four points outside the top four.

The second-last placed Lions overcame the suspension of assistant coach Leon Boshoff for a verbal spray after last week's thrashing by the Stormers which reportedly included a comment that the side's black players would "go far because of their skin colour".

"We just didn't finish them off. We had plenty of opportunities, our execution was poor and we didn't capitalise on our opportunities," Friend told AAP.

"We didn't put them under enough pressure."

Asked if there was any reason for that, Friend said: "No, sometimes you have off nights."

But Friend was satisfied with his side's set-piece work and praised Mark Gerrard's kicking game as the former Test winger continued a strong season in the No.15 jersey.

The Brumbies head to the Indian Ocean city of Durban on Sunday to prepare for the crucial clash with the second-placed Sharks, who will return home with a 3-1 haul from their Australasian tour.

Friend said he didn't expect the travel home to affect the Sharks, just as he wasn't using the 14-hour flight as an excuse for the Brumbies' first-up loss in their three-game trip to the Republic.

"If you let travel be an issue, it becomes an issue," he said.

"You jump on a plane and get home and sleep well and recover from it for a couple of days, you're fine.

"That's not the reason why we didn't win."

After falling behind to a second-minute Gerrard penalty goal, the Lions hit back through tries to Springbok centre Jaque Fourie and livewire halfback Jano Vermaak to grab a 12-3 advantage.

Lions skipper Cobus Grobbelaar was sin-binned moments before halftime and Mortlock took advantage to score a soft try which Gerrard converted.

Andre Pretorius responded with a drop goal to have the Lions up 15-10 at halftime.

The Brumbies regained the lead soon after the break when lock Mark Chisholm charged down a Pretorius kick and regathered to dive over for a try that Mortlock converted.

A Pretorius penalty goal on 51 minutes gave his team an 18-17 advantage before Ludik pounced to score after the Brumbies had lost the ball attempting to launch a late attacking move.

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