The team will be tested again tomorrow, after which a decision on their travel plans will be made.
South Africa claimed bronze at the Rio Olympics and will be strong medal contenders in Tokyo. They are scheduled to face Ireland and Kenya on day four of the Olympics.
"We are in a good space, despite the upheavals we encountered once we arrived," Springbok Sevens coach Neil Powell told Springboks.rugby.
"We have made a commitment to each other when we started this campaign that we will be mentally strong as well and that was tested with this episode. Adaptability – both mental and physical – will be key at this Olympics and we already felt that when we arrived.
"We took a knock, but I can say the players took in their stride. We can only control the controllable, so we remain positive. We will still have a training session while we wait for clearance, the only difference is it will be via Zoom call with the players in their rooms."