49ers CEO Jed York tweeted early Monday morning that Harbaugh, who played quarterback in the NFL for 13 seasons, would be throwing passes to Moss at the workout.
"Former Colt Pro Bowl QB throwing for #49ers tomorrow. Just to clarify, Coach Harbaugh is turning into Capt Comeback to throw to Randy Moss," York wrote.
On Monday afternoon, York took to Twitter again and called the session the "Best coach's workout in NFL history (especially while wearing khakis & a sweatshirt)."
Harbaugh is standing in because a current 49ers quarterback can't throw in a workout for the team until the league year begins Tuesday at 4 p.m. ET.
"I talked to Jim tonight," York told SI.com on Sunday night. "He's excited and a little nervous. He's a competitive guy. He doesn't want to look bad."
The 35-year-old Moss is attempting to make an NFL comeback after a year out of pro football.
Moss, who worked out last Tuesday with the New Orleans Saints, played for New England, Minnesota and Tennessee in a rocky 2010 season. He could help fill a big void after 49ers receivers managed just one catch for three yards in a 20-17 overtime loss in the NFC Championship Game to the eventual Super Bowl champion New York Giants.
Moss' workout with the Saints was said to be impressive, according to reports. The Saints didn't publicize details of the session.
San Francisco cut ties with Braylon Edwards in December and already was without Joshua Morgan, who broke a bone in his lower leg Oct. 9 against Tampa Bay, had surgery to have screws inserted and was placed on season-ending injured reserve. Morgan is expected to generate his share of interest in free agency.
Michael Crabtree, San Francisco's 10th overall pick in the 2009 draft, had 72 receptions for 874 yards and four touchdowns.
Moss' best season came with the Patriots in 2007, when he caught 98 passes for 1,493 yards and a single-season-record 23 touchdowns in helping New England to a 16-0 regular-season record.
He has 954 catches for 14,858 yards and 153 TDs in his 13-year career, which included a stint in the Bay Area with the Oakland Raiders in 2005 and '06. Moss also has had more than 1,000 yards receiving in a season 10 times, second only to Hall of Famer Jerry Rice, who did that 14 times.
York said 49ers need "someone to stretch the field."
York also said the 49ers are working to re-sign the man who could be throwing to Moss next season, quarterback Alex Smith. York said the side have had "good conversations back and forth."
The 49ers CEO also announced that the team tendered one-year contracts to exclusive rights free agent cornerback and special teams player Tramaine Brock and restricted free agent linebacker Larry Grant.
Brock has appeared in 14 games in two seasons, while Grant became a key fill-in last season on Vic Fangio's defense while All-Pro linebacker Patrick Willis nursed a hamstring injury.
Information from The Associated Press was used in this report.