In a statement released on his personal website he announced the girls had been named Charlene Riva and Myla Rose.
"I have some exciting news to share with you," Federer said on his Facebook page.
"Late last night, in Switzerland, Mirka and I became proud parents of twin girls."
"This is the greatest day of our lives. Mirka, Myla and Charlene are all healthy and doing very well."
It was the first children for the couple who got married in April.
The 27-year-old Federer, who clinched his 15th Grand Slam in Wimbledon to break Pete Sampras' record, met his wife in 2000 at the Sydney Olympic Games.
Mirka, 31, emigrated with her family to Switzerland from Slovakia when she was two after playing on the WTA Tour. She retired prematurely due to injury and became one of Federer's managers.
Deccan Herald is on WhatsApp Channels| Join now for Breaking News & Editor's Picks