The 32-year-old world number four said he has been suffering a problem with his left knee which needed treatment in his Wimbledon first round loss to Daniil Medvedev last month.
"After much backwards and forwards and consultations with my doctors and my team unfortunately I have decided to skip Canada and Cincinnati to be on the safe side even though I've been battling hard to make these events," Wawrinka wrote on Facebook.
"Hugely disappointing for my fans and myself that I have to make this decision, but I need to be 100 per cent confident before I resume competition till the injury that plagued me in Wimbledon has been resolved.
"My team and I are doing everything possible to make this a speedy recovery."
The US Open, the final Grand Slam event of the season, starts in New York on August 28th.
Wawrinka joins former world number one Novak Djokovic on the sidelines after the 12-time major winner called time on the rest of his season to rest a elbow injury.