Donnie took a chest knock in the loss to the Springboks at the ABSA Stadium last weekend.
Scotland skipper Jason White worked separately with the medical team, he is also expected to be fit for Saturday's second test.
Glasgow Warriors No 8 John Beattie, however, did not train. He remained at the team hotel having been laid low by a stomach bug.
But now the Scotland boss is hoping the virus will not spread ahead of the game and decimate his squad.
Frank Hadden said: "We are just praying this is not the tip of an iceberg.
"There is a bug doing the rounds and the obvious concern is it will develop into something bigger.
"Johnny is not the only one who has been affected, but he was too sick to do any training.
Among the backs Hugo Southwell, who had taken a knock to his neck/shoulder last weekend, also completed the full training session today.
Wing Sean Lamont (leg injury) did mainly straight-line running with the medical team at today’s open training session. Coach Frank Hadden said: "Sean is better than expected. We felt there was no chance of him playing in the second Test earlier in the week. There is a glimmer of hope there now. We'll be monitoring him over the next 24 hours."
John Beattie's illness will also be monitored carefully in case any other members of the party come down with a similar bug. It also means any decision on whether John can be released to join up with the Scotland under-21 squad in France cannot be made until the overall health of the squad in South Africa is ascertained.