Harbaugh had been expected to leave the franchise at the end of the season and confirmation arrived shortly after the 20-17 win over the Arizona Cardinals on Sunday that brought their campaign to an close.
The 49ers missed the playoffs for the first time in four seasons under Harbaugh, finishing the year 8-8 to leave his overall record with the team at 49-22-1, including post-season results.
Harbaugh, who built his coaching career in the college ranks with Stanford, is expected to be named as the next coach of the University of Michigan, his alma mater, later this week.
“This has been the time of my life, [like] that song,” Harbaugh said. “I had a lot of fun. It’s the relationships that were made along the way. That’s what a team is. And I appreciate the fans, the people of the Bay Area, the 49er Faithful. All the good times that we’ve had.
“I think it’s been really good and fantastic. Players, coaches, staff, friends for life.”
Harbaugh is the first of what could be a record number of coaches to be released from their contracts, with Chicago Bears coach Marc Trestman and New York Jets chief Rex Ryan among those whose jobs are in serious danger on what has become known as ‘Black Monday’.
Atlanta Falcons coach Mike Smith is also on the chopping block after his team failed to make the playoffs on Sunday when they were thrashed 34-3 at home by the Carolina Panthers in a divisional decider.