The surgery will be performed on Monday by Cincinnati Reds team doctor Tim Kremchek.
Guzman, who did not play at all this season, was placed on the 15-day disabled list on March 27. He planned to get better with rest and rehabilitation.
"I have worked day and night the last two months to rehab my shoulder and get back on the field, but unfortunately, it did not respond to the extent we'd hoped," Guzman said on the team's Web site.
"Cristian worked extremely hard to attempt to get back without surgery," General Manager Jim Bowden told the Washington Post. "It was evident that we have no choice but to operate and get him ready for next year. He's been trying to get through it and kept trying to strengthen it. At times it felt OK, but it's just not there. He just can't do it."