Spain's Nadal had said in June that he had reservations about travelling to the US amid the Covid-19 pandemic and he joins women's world number one Australian Ash Barty in skipping the tournament due to Covid-19 concerns.
"After many thoughts I have decided not to play this year's US Open," Nadal said on Twitter.
"The situation is very complicated worldwide, the Covid-19 cases are increasing, it looks like we still don't have control of it.