Nadal's bid for a 13th French open title suffered a setback.
The US Open champion had already been having fitness issues while in New York.
The former world number one is still making his way back up the ranks after a major surgery in 2019.
A new Grand Slam champion will be crowned for the first time since Marin Cilic won the US Open in 2014.
The 33-year old Serbian is eager to win his 18th Grand Slam at the Flushing Meadows this year.
Meanwhile, Spain's Marcel Granollers has replaced France's Benoit Paire in the men's singles draw.
The Serbian world number one is eyeing his 18th Grand Slam title with the US Open starting on August 31.
The Western and Southern Open is being played in New York this year in preparation for the US Open.
The 33-year old Serbian is currently three short of Federer's 20-Grand Slam tally, and two short of Nadal's 19 major titles.
WTA world number one Ashleigh Barty, fifth-ranked Elina Svitolina, and number seven Kiki Bertens have already pulled out of the 2020 US Open.
Nadal is the latest high profile player to pull out of the Grand Slam event.
Spanish health ministers have recommended the cancellation of the event amid the novel coronavirus pandemic.
Whether they play the US Open remains to be seen.
The tennis season has been at a standstill since mid-March due to the virus outbreak worldwide.
Last week world number three Dominic Thiem said that the tournament was "on shaky legs."
Despite the coronavirus risk, the French Open will not be played behind closed doors.
The Spain For Sure campaign wants to send out a message that the country is now a safe travel destination, after the coronavirus outbreak.
Players will be undergoing daily temperature checks along with two COVID-19 tests every week during their stay in the USA
The 38-year old Swiss star is running out of opportunities and his fans are unsure whether he will appear in Wimbledon again.
The newly rescheduled French Open clashes with the timings of several ATP and WTA tournaments
Either Thiem or Zverev will face Federer or Djokovic in the Australian Open 2020 Final
The 16-time Grand Slam winner is aiming to lift his 8th Australian Open title