"My knee is much better and the rehabilitation process has gone well as predicted by the doctors, but this virus didn't allow me to practise this past week," Nadal, 26, said.
"Therefore I am sorry to announce that I will not play in Doha and the Australian Open, as we had initially scheduled."
The Spanish number one and world number four has not played competitive tennis since his surprise second-round Wimbledon exit to Lukas Rosol in June.
He was since diagnosed with a partial tear of the patella tendon and inflammation in his left knee and was unable to defend his Olympic title at the London Games.
The 11-times Grand-Slam champion also missed the US Open and season-ending World Tour Finals before returning to the practice court on November 20.
But he withdrew from the exhibition tournament in Abu Dhabi this week, citing illness, having earlier admitted he would be short of full fitness until the start of the clay-court season in the Spring.
There has been ongoing speculation that the world number four's career may be in decline due to impact-related knee injuries suffered as a result of his all-action game.
He is expected to attempt to play at the 2013 French Open, the only clay-court Major. But the harder courts of Melbourne, Flushing Meadows and even Wimbledon could prove too damaging for the Majorcan.