Nadal said that he would not play in Brisbane because of a left thigh strain, prompting yet more fears over the 32-year-old's long term future in tennis.
Nadal, who claimed his 17th Grand Slam title at Roland Garros last year, has not played a competitive match since September.
He also lost the world number one ranking to Djokovic, whose battles with the Spaniard are one of modern sport's greatest rivalries.
"He has done the comebacks for so many times in his career that you always believe that he can do it again," said Djokovic after reaching the Qatar Open quarter-finals on Wednesday.
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"He has a very physical style of tennis which obviously is putting a lot of load and pressure on his joints, on his knees.
"Sport needs Rafa, no question about it. He is one of the greatest legends of all time and we want to see him play."
Djokovic and Nadal have met in the finals of all four of the Grand Slams and 52 times in total.
Among their most memorable matches was the 2012 Australian Open final, lasting almost six hours and won by the Serb.
A 2013 French Open semi final was dubbed the greatest ever match on clay and last year battled again for more than five hours in a Wimbledon semi-final.
They first met in on court in Paris in 2006 when, ironically, Nadal was declared the winner after Djokovic had to retire during the match with injury.
Nadal, the current world number two, has not played a main tour event since a knee problem forced him to retire during his US Open semi-final against Juan Martin del Potro in September last year.
The 32-year-old had surgery on his ankle in November and only resumed training three weeks ago.
Nadal said doctors were confident he would be fit to play at the Australian Open which starts on January 14.
"They say that it's a very small thing, but it can become a big thing, because a strain in the muscle is dangerous," he said.
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