Team spokesman Bob Lange confirmed the deal in a text message to The Associated Press early Wednesday. Terms were not disclosed.
The former Texas Tech star is the only draft pick who had yet to sign.
Crabtree could provide the game-breaking wide receiver threat the 49ers have been lacking, assuming he can quickly learn the offense after missing all of training camp. The 10th pick overall, he also sat out offseason minicamps and organized team activities while recovering from a foot injury, but was a regular presence at the team's training facility.
The 22-year-old Crabtree and his agent, Eugene Parker, sat down with three top 49ers officials Tuesday in an attempt to work through his contract impasse. Crabtree had balked at a longstanding offer of approximately five years and $20 million with a reported $16 million guaranteed, instead seeking money comparable to higher draft picks.
Coach Mike Singletary acknowledged last month that the 49ers discussed changing their offer to Crabtree, and team president Jed York said in mid-September that the team hoped for a face-to-face meeting with Crabtree but hadn't heard back from his representatives.
That meeting finally happened Tuesday at an undisclosed spot in the Bay Area away from the team's Santa Clara headquarters. Crabtree and Parker were joined by York, vice president of football operations Paraag Marathe and general manager Scot McCloughan.
It's not common for a player to join such contract talks.
Singletary, whose team leads the NFC West and at 3-1 is off to its best start since 2002, said Monday he would welcome Crabtree whenever he shows up to join the team.
The 49ers must sign Crabtree by Nov. 17 for him to remain eligible to play this season. The team would have a seven-week window before the 2010 draft to trade Crabtree if he did not sign.
Crabtree caught 97 passes for 1,165 yards and 19 touchdowns last year during his sophomore season at Texas Tech. He finished his college career with 231 receptions for 3,127 yards and 41 touchdowns.