"Wished we could've finished the job!!thanks for the opportunity an good luck in the future 9ers," the receiver tweeted Saturday evening.
The 36-year-old Moss, who ended his one-year retirement to play for the 49ers last season, played in all 16 games for San Francisco in 2012.
Moss had 28 receptions for 434 yards and three touchdowns in 2012 for the NFC champion 49ers. He caught two passes for 41 yards in San Francisco's Super Bowl loss to the Ravens.
He has 982 catches for 15,292 yards and 156 touchdowns in his 14-season career.
Moss enjoyed his best season 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.
Information from The Associated Press was used in this report.