Nadal hasn't played in an ATP tournament since late June when he was stunned in the second round at Wimbledon.
He has said the knee injury has healed but withdrew from this week's exhibition in Abu Dhabi because of a stomach illness. The same illness will keep him on the sidelines for the Australian Open.
"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 practice this past week and therefore I am sorry to announce that I will not play in Doha and the Australian Open, as we had initially scheduled," Nadal said in a Facebook posting.
"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.
"I will have to wait until the Acapulco tournament to compete again although I could consider to play before at any other ATP event."
Nadal was the runner-up to Novak Djokovic in last year's Australian Open. He won the event in 2009.