He was to have met Australian Alex de Minaur in the Washington quarter-finals on Friday.
"I’m exhausted after playing so much over the past four days, having not competed on the hard courts for 18 months.
I also need to be careful and to listen to my body as I come back from a long-term injury," Murray said in a statement.
"I’m gutted not to be playing and I’d like to thank the tournament and all the fans.
"There are lots of positives to take from this week, so I’ll take some time to rest and recover, and then head to Cincinnati early to prepare and get ready."
In his third tournament back from hip surgery in January, the Scot showed signs of improvement, reaching his first quarter-final in more than a year.
The 31-year-old captured all three of his victories in three sets, the first time he has won three consecutive deciding sets at the same event since winning the 2016 Queen's Club tournament.
An emotional Murray broke down in tears after coming from behind to defeat Marius Copil 6-7(5) 6-3 7-6(4) in a marathon third round match that lasted more than three hours on Thursday.
(Reporting by Gene Cherry in Raleigh, North Carolina; Editing by Ian Ransom)
