Scoppetta had the operation Tuesday after tests confirmed he had a blocked coronary artery.
The 70-year-old commissioner was resting comfortably, said Jim Long, a department spokesman.
"He is in very good spirits," Long said. "He's feeling well."
Scoppetta will work from home via fax, phone and e-mail and will return to the office sometime in the next week, Long said.
Scoppetta served as former Mayor Rudy Giuliani's chief of the Administration for Children's Services.
He was named fire commissioner by Mayor Bloomberg on Dec. 30.
Bypass surgery, which dates back to the 1950s, is now a common procedure in cases when coronary arteries are blocked.
The arterial graft is typically taken from the patient's leg.
The blockage in Scoppetta's artery showed up during a routine stress test during his annual physical, the fire spokesman said.
