Gwynn, wife, Alicia, told ESPN.com that doctors performed a complex nerve-graft procedure, in which they removed a facial nerve and replaced it with a nerve from Gwynn's shoulder.
Alicia Gwynn said the surgery concluded at about 1 a.m. PT Wednesday, and that doctors said they had removed the cancerous growth from his parotid gland in its entirety. The surgery was performed at Moores Cancer Center at the University of California-San Diego.
"All is well -- it doesn't seem like last time," Alicia Gwynn told ESPN.com. "It turned out great. He looks good, he looks normal. His eyelids are a little swollen, but they got all the cancer. They say they got it all. His face looks good. They did an amazing job."
There were no signs of complications and all biopsies performed during the operation came back negative, she said. The nerve graft came with the risk that Tony Gwynn's face could have been partially paralyzed or disfigured.
"He's a little drowsy now, and we'll be talking to the doctors again, but, yes, the biopsies were clear," Alicia Gywnn said.
Tony Gwynn, 51, is the baseball coach at San Diego State. His wife said she believes he will be able to resume coaching in about a month.
"Our thoughts and prayers are with Tony and his family today," Padres vice chairman and chief executive officer Jeff Moorad said on Tuesday. "Tony has a fighting spirit and we have faith that he will continue to battle this disease with the same perseverance that was the hallmark of his playing career. We know Mr. Padre has all of San Diego rooting for him."
Gwynn, an eight-time National League batting champion during a 20-year career with the Padres, was diagnosed with cancer of the parotid gland in August 2010. He's had three surgeries since 1997 to remove tumors on the gland.
Gwynn has maintained that chewing smokeless tobacco played a role in him developing cancer.
Gwynn finished his playing career in 2001 with 3,141 hits and a career .338 average. He was elected into the Hall of Fame in 2007.