Crabtree was operated on Wednesday, one day after suffering the injury during an organized team activity.
"Michael Crabtree underwent surgery to repair his Achilles tendon that he tore yesterday," coach Jim Harbaugh said. "Surgery was successful and we do not anticipate it will be season-ending for Michael."
Harbaugh would not speculate when Crabtree might return to play.
The 25-year-old Crabtree, the team's 10th overall pick in the 2009 draft out of Texas Tech, had career highs last season with 85 receptions for 1,105 yards and nine touchdowns for the NFC champion Niners, who lost 34-31 to the Baltimore Ravens in the Super Bowl.
USA Today first reported that Crabtree was hurt during Tuesday's OTA, citing an unidentified source.
This could be a major setback for the two-time defending NFC West champions after Crabtree's breakout 2012 season. He was one of the big reasons the franchise returned to the Super Bowl for the first time in 18 years, clicking with quarterback Colin Kaepernick after his promotion to starter in November over departed 2005 No. 1 overall draft pick Alex Smith.
Kaepernick and Crabtree were eager to get back on the field together after falling just short in New Orleans back in February.
Kaepernick's fourth-down throw into the end zone in the closing moments sailed over Crabtree. Harbaugh and the 49ers argued that Crabtree got held, bumped by cornerback Jimmy Smith with safety Ed Reed trailing the play.
Crabtree also had five TDs and 30 catches on third-down plays last season - both stats among the top five in the NFL.
He has bounced back the past two seasons from several injuries.
After a 71-day contract stalemate as a rookie, Crabtree was sidelined during the 2010 preseason with a neck injury. Again a year later he was out with a broken foot sustained while working out in Alex Smith-organized practices during the NFL lockout.
In 2011, Crabtree led the team in catches (72) and yards receiving (874), but San Francisco came up short of a Super Bowl.
While he had four catches for 25 yards and a 4-yard touchdown reception in a 36-32 victory against Drew Brees and the favored Saints in the NFC divisional playoffs, it was the NFC championship game Crabtree remembers as a most disappointing day.
San Francisco's receivers had just one catch for 3 yards - yes, it was by him - and Crabtree was targeted four times in a 20-17 overtime loss to the eventual Super Bowl champion New York Giants.
Crabtree said that performance helped fuel him last year.
Notes: The 49ers signed fourth-round draft pick WR Quinton Patton to a four-year contract. ... The team also claimed tight end/long snapper Kyle Nelson off of waivers from the San Diego Chargers and waived P Anthony Santella.