San Francisco placed Morgan on the season-ending injured reserve list Wednesday after he was hurt late in a 48-3 victory against the Tampa Bay Buccaneers last Sunday. To help fill the void, the Niners signed wideout Brett Swain to a one-year deal.
Coach Jim Harbaugh said Monday he still was hopeful that Morgan might return late in the season or for a possible playoff game, but Morgan had been scheduled for surgery on the leg.
The 26-year-old Morgan, a fourth-year pro out of Virginia Tech, has 15 catches for 220 yards and one touchdown for the 49ers (4-1).
Also Wednesday, San Francisco released center Chase Beeler from the practice squad.