Federer, the champion in Paris in 2009 and the holder of a record 17 Grand Slam titles, pulled out of the French Open after failing to recover from the knee and back injuries which have decimated his season.
The bombshell means the 34-year-old will miss a Grand Slam event for the first time since 1999, ending a run of 65 consecutive major appearances.
"It makes me sad and it's scary. It's bizarre to say that he won't be in Paris," said Wawrinka, a longtime friend of Federer with whom he has won Olympic doubles gold and the 2014 Davis Cup.
"It proves that we are never safe from injury," the 31-year-old Wawrinka told the ATS news agency.
"It's sad for tennis, a big blow for his fans and especially for him as he's had a very difficult season."
Wawrinka, who is playing at this week's Geneva Open tournament to warm up for his Roland Garros title defence, hailed Federer's stunning longevity.
"His 65 consecutive Grand Slam appearances are the kind of statistics that allows everyone to see everything he has accomplished."
Switzerland's 1992 Olympic champion Marc Rosset said he was not surprised by Federer's decision.
"He only trained for 10 minutes on Wednesday," Rosset told ATS.
"It's a shame that his sequence of 65 Slams has finished. A Roland Garros without Federer, it will be bizarre.
"But I am not despondent by this because he could not have won in Paris this way but I would have been destroyed if he had pulled out of Wimbledon (where Federer has seven titles).