Rossi, 41, returned a "positive with very low viral load" COVID-19 result on Tuesday, but tested negative for the novel coronavirus on Wednesday and Thursday.
"Both follow-up tests came back negative for the COVID-19 virus, confirming Rossi's attendance for this race weekend," Yamaha said in a statement.
The Italian earlier missed two races at Spain's MotorLand Aragon circuit in October after contracting the virus but was cleared to race in the European GP last weekend, where he pulled out on lap five due to a mechanical failure.
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Rossi has not finished a race since the San Marino Grand Prix at Misano at the start of September and sits 15th in the championship standings with 58 points.
Suzuki's Joan Mir holds a 37-point lead in the championship heading into the penultimate race in Valencia on Sunday. (Reporting by Manasi Pathak in Bengaluru Editing by Toby Davis)
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