Nadal overcame Tsitsipas in the Rogers Cup final on Sunday in Toronto, beating the Greek 6-2, 7-6 (7-4).
The world No 1 had been handed a bye for the first round of the Cincinnati tournament but announced that he would not be competing in the event.
“I am very sorry to announce that I won’t be playing in Cincinnati this year,” Nadal said in a statement.
“No other reason than personally taking care of my body and trying to keep as healthy as I feel now.
“I am very thankful to my friend Andre Silva, Tournament Director of the Cincinnati tournament, who after speaking to him on the phone understood what I said to him and understands the situation.
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“I am sure the tournament will be a success and I wish him and his team all the best.”
By winning in Toronto, Nadal took his career haul of Masters titles to 33.
In doing so, he became the first player to book his spot at the year-ending ATP World Tour finals in London.
And after securing his 80th ATP Tour title, Nadal revealed he wished he had played more in Toronto.
“There have been many years without coming back to Toronto and I miss this tournament a lot,” Nadal said.
“I have had too many injuries in my career to come here more often, but this week has been fantastic.
“To receive this trophy means everything to me.
“And to have the support of you for the whole week means I wake up every morning and I practice every day on court with the highest amount of passion possible.”
With his withdrawal from the Cincinnati Masters, it leaves Nadal with a little more chance of preparation ahead of the US Open.
The final Grand Slam of the year begins on August 27 with the 32-year-old looking for his fourth title at Flushing Meadows.
Nadal won the tournament last year, beating Kevin Anderson in the final.