Prudhomme left the race last Tuesday after testing positive for COVID-19, saying he would be back after a week provided his new test came back negative.
The 59-year-old, who had been replaced by interim Tour director Francois Lemarchand, did not show any symptoms.
The rules in place this year state that should a team have two positive cases, the whole outfit will be thrown out of the race.
Four teams had one case of coronavirus within their ranks but they were allowed to stay on the race.
The results of the second round of tests will be unveiled later on Tuesday before the start of the 16th stage.
Meanwhile, yellow jersey holder Primož Roglič (Jumbo-Visma) has confirmed that he and his team have tested negative for COVID-19, after the second round of tests.
"They said that we were negative, so I'm happy that we have one more week of racing," Roglič said.
However, a (umbo-Visma team spokesman remained cautious as he said the results of the staff members were not out yet.
"We are not allowed to confirm that," he said.
"Anyway, not all our results are known yet."
Roglič leads by 40 seconds ahead of Tuesday night's (AEST) mountain trek between La Tour du Pin and Villard de Lans.
The Tour de France will return for Stage 16 tonight LIVE, FREE and EXCLUSIVE at 8:55pm (AEST) tonight, via the SBS ŠKODA Tour Tracker, and at 9:30pm (AEST) on SBS VICELAND and SBS On Demand.