The Austrian spent four days in bed with a virus after pulling out of a tournament in Doha last week.
Canada's Milos Raonic has withdrawn from the ATP Tour Finals in London due to injury and been replaced by Spain's David Ferrer.
Roger Federer, who will be chasing an 18th Grand Slam title at the Australian Open later this month, breezed through to the Brisbane International men's semi-finals with a 6-1, 6-1 thumping of Australian Marinko Matosevic.
In his pre-tournament news conference in Toronto on Sunday, Nadal said a recurring foot issue he has been dealing with since 2005 returned at the French Open, where he fell to eventual champion Djokovic in the semi-finals.
Swiss second seed Stan Wawrinka advanced into the semi-finals at the Rogers Cup with a comprehensive 6-1, 6-3 victory over big-serving South African Kevin Anderson at the Aviva Centre in Toronto on Friday.
Stanislas Wawrinka trumped fellow Swiss Roger Federer at a grand slam for the first time with a 6-4, 6-3, 7-6(4) victory in the French Open quarter-finals on Tuesday.
Second Andy Murray breezed to a 6-3, 6-0 semi-final victory over Kei Nishikori on Saturday to set up a final with Novak Djokovic at the Rogers Cup in Montreal.
The 32-year-old world number 18 still had a remote chance of qualifying for the season-ending ATP World Tour Finals for an eighth time.
Rafael Nadal looked something close to his old masterful self on clay again as he crushed Czech Tomas Berdych.
With 1,500 points available for an undefeated champion next week, the tournament could produce a thrilling climax with Murray and Djokovic, who have never met at the O2, facing off in the final for the year-end number one ranking.
Andy Murray's runstellar stretch included his second Wimbledon title, second Olympic gold medal and wins at Queen's Club and Rome.
Nadal, Djokovic, Murray, Wawrinka all will be in action at Roland Garros on Wednesday
French Open champion Stan Wawrinka has become the fourth player to qualify for the season-ending ATP World Tour Finals in London.
Zverev's brother Mischa Zverev was also eliminated, going out 6-3, 6-1 to David Ferrer in the first round, while Kei Nishikori eased to a 7-5, 6-2 win over Taylor Fritz to secure a place in the third round.
Defending champion Rafael Nadal remains on course for an 11th Monte Carlo Masters title after beating Bulgaria's Grigor Dimitrov 6-4, 6-1 in the semi-finals on Saturday.
Having dug in early on to stay with Federer, Nishikori ended up running away with the match to inflict a first straight sets defeat in the ATP Finals round-robin stages on the 20-time Grand Slam champion.
Croatian ninth seed Marin Cilic reached the Wimbledon quarter-finals for the third year running after Kei Nishikori quit with a rib injury midway through their fourth round match on Monday.
With Roger Federer missing due to injury, Andy Murray upset in the quarters and Rafael Nadal a fourth-round loser, Djokovic marches on in a quest for a 13th Grand Slam title without his familiar high profile rivals standing in the way.
Argentine Juan del Potro has withdrawn from next week's Brisbane International due to a persistent left wrist injury, tournament officials announced on Thursday.
A round-up of results from Davis Cup matches played on and Sunday
Fourth seed Rafael Nadal survived a few anxious moments before booking his place in the semi-finals of the BNP Paribas Open with a see-sawing 6-4, 6-3 victory over Japanese Kei Nishikori at Indian Wells in California on Friday.
Rafael Nadal struggled to finish off Fabio Fognini at the Barcelona Open on Friday but eventually quelled one of his most troublesome opponents 6-2, 7-6(1) to reach the semi-finals.
Japan's Kei Nishikori cut short Marin Cilic's title defence with an impressive 4-6, 7-6 (0), 6-2 win on Monday.
Andy Murray demolished Croatian teenager Borna Coric 6-1, 6-2 in the second round of the Paris Masters on Wednesday to set up a Davis Cup-flavoured clash with Belgium's David Goffin.
Swiss tennis star Martina Hingis has said that Li Na's retirement was a loss to world tennis, while also crediting the Chinese ace of raising the game's profile in her home country and across Asia.
Spain's David Ferrer, his eyes fixed on qualifying yet again for the ATP World Tour Finals, romped past fellow Spaniard Guillermo Garcia-Lopez 6-1, 6-1 to reach the quarter-finals of the Vienna Open on Thursday.
18-year-old Carlos Alcaraz earned his first ATP Masters 1000 crown
Also in action on the first day at Roland Garros is men's second seed Alexander Zverev who meets Ricardas Berankis of Lithuania on Court Suzanne-Lenglen.
Croatian Ivo Karlovic hit a record 45 aces en route to beating third seed Tomas Berdych and reach the Halle Open semi-finals on Friday.
Milos Raonic of Canada will take on defending champion Novak Djokovic in the final of the Paris Masters.
World number one Andy Murray shrugged off a sluggish start to reach his fifth French Open semi-final with a 2-6, 6-1, 7-6(0), 6-1 defeat of Japan's Kei Nishikori.
Photos from the ATP World Tour Finals matches played in London on Tuesday.
Defending champion Novak Djokovic was beaten 7-6(6) 6-1 3-6 7-6(5) by American Sam Querrey in the Wimbledon third round on Saturday. The Serbian top seed trailed by two sets overnight after the Court One match was interrupted by rain on Friday and there was no escape for the 29-year-old as Querrey, the 28th seed, completed a huge shock.
With the Australian Open currently on, defending champion Novak Djokovic has once again been dubbed as a favourite to retain the title, and former world No. 17 Bernard Tomic of Australia firmly believes there will be no one to challenge the great Serbian.
Roger Federer's hopes of knocking Novak Djokovic off the top of the ATP world rankings before the end of the year took a hit when he lost to big-serving Canadian Milos Raonic in the Paris Masters quarter-finals on Friday.
British tennis maestro Andy Murray has reclaimed his second spot from Roger Federer in the latest ATP rankings after winning his maiden Italian Open title.
World number two Roger Federer edged past Ivo Karlovic 7-6(3), 7-6(4) on Saturday to reach the Halle Open final and stay on course for his eighth title in the grasscourt Wimbledon warmup event.
Nadal, who is the clear tournament favourite and looks to be in the form of his life on clay this season, raced into a 3-0 lead before Spanish compatriot Almagro felt his left knee with less than half an hour played.
Maria Sharapova joined Serena Williams in making an early exit from the Australian Open on Monday but defending champion Victoria Azarenka swept into the quarter-finals with an 18th straight victory at Melbourne Park.
Andy Murray could beat Roger Federer on Thursday and crash out of the ATP World Tour Finals or lose and go through to the semi-finals -- such is the conundrum he faces.
