"I am very disappointed that I will not be able to compete this year in Abu Dhabi," Nadal said in a statement. "I was really excited about returning to play and I always have a wonderful experience at the event and this is the first time I will miss the tournament."
Nadal was to join world No. 1 and defending champion Novak Djokovic, Serbian countryman Janko Tipsarevic, the Czech Republic's Tomas Berdych, Briton Andy Murray and Spain's David Ferrer at the winner-take all $250,000 event, which begins Thursday.
With the 11-time Grand Slam winner's decision to pull out, Nadal will be replaced by "another top player," tournament director Greg Sproule said.
Nadal, who was planning on using the event as part of his rehabilitation from a knee injury, said the decision to skip the three-year Abu Dhabi event was made by doctors.
"My rehab has gone well, my knee feels good and I was looking forward to competing," he said. "Unfortunately, doctors have informed me that my body needs to rest in order to fight this stomach virus."