Rossi missed the Aragon double header last month after contracting the virus between the French and Aragon Grand Prix.
After initially testing positive again last Tuesday, Rossi passed the other tests he had to take and was able to take part in the European Grand Prix last weekend.
However, on Tuesday after his return to Italy, Rossi tested “positive with a very low viral load” and was recommended by doctors to do two more tests.
The first shot on Wednesday gave a negative result on Thursday, while the next shot this morning also gave a negative result.
Rossi has now been cleared for participation in the Valencia GP this weekend with his crew after all relevant tests have been completed.
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A Yamaha source had confirmed the previous Thursday that the Japanese manufacturer would not provide a replacement for Rossi this weekend if he had not been able to take part in the race.
Last week, Yamaha put American World Superbike rider Garrett Gerloff on standby to replace Rossi in case he missed the European GP.
Since Rossi was not released to drive in time for Friday’s practice session, Yamaha Gerloff used the motorcycle for both sessions.
The American impressed, ending the day just 1.5 seconds behind the pace on the combined timesheets.
Yamaha will be missing members this weekend after five team members – including team manager Massimo Meregalli – were forced into quarantine last week when one of Maverick Vinales’ employees tested positive for COVID-19.
This followed last month when six Yamaha members were quarantined ahead of the French GP when one tested positive for COVID-19.
Rossi’s first race since the French GP last weekend ended after just five laps due to a technical problem.
This was a bad phase for the Italian, who has not seen the checkered flag since the San Marino Grand Prix in Misano in early September.
Tech 3 rider Iker Lecuona was also cleared for this weekend from Saturday after being forced to miss the final race when his brother tested positive for the virus.