The 26-year-old Spaniard said Friday he has been forced to withdraw from the Grand Slam event from Jan. 14-27 and the preceding Qatar Open at Doha.
The same virus kept him from making his return at Abu Dhabi this week.
Nadal said his decision to withdraw from the two events had nothing to do with the tendinitis in his left knee, which made him take a hiatus since last summer following his second-round loss to then 100th-ranked Lukas Rosol at Wimbledon in June.
"My knee is much better and the rehabilitation process has gone well as predicted by the doctors," Nadal said in a statement from his hometown of Manacor on the island of Mallorca. "But this virus didn't allow me to practice this past week and therefore I am sorry to announce that I will not play in Doha and the Australian Open."
The former No. 1 said he hopes to make his long-awaited return at Acapulco starting on Feb. 27. However, he did not rule out playing at an earlier tournament if his recovery went well.
"As my team and doctors say, the safest thing to do is to do things well and this virus has delayed my plans of playing these weeks," said Nadal. "I always said that my return to competition will be when I am in the right conditions to play and after all this time away from the courts I'd rather not accelerate the comeback and prefer to do things well."
Nadal's doctor, Angel Ruiz-Cotorro, said in the same statement that Nadal needed at least a week to recover from the virus, ruling him out for the Qatar Open set to start on Jan. 2.
And Nadal's coach and uncle, Toni Nadal, explained that Nadal had then opted against making his return at Melbourne since he wouldn't be physically fit to take on its five-set format.
"We consider not appropriate to play the Australian Open since we will not have enough preparation for a greater competition which is a Grand Slam tournament," said Toni Nadal in the statement. "It is simply not conceivable that his first event is a best of five sets event, he wouldn't be ready for that."
Nadal's knee injury prevented the 11-time Grand Slam winner from defending his Olympic singles gold at last summer's London Games, where he was supposed to be Spain's flag bearer in the opening ceremony. He also had to pull out of the U.S. Open and Spain's Davis Cup final against the Czech Republic, which his teammates lost without him.
Nadal, who is currently ranked fourth, won the Australian Open in 2009. Last year, he lost to top-ranked Novak Djokovic in an epic final that lasted five hours and 53 minutes, the longest ever match at the event and the longest men's Grand Slam final on record.