SANTA CLARA, Calif. -- Jim Harbaugh and the 49ers have mutually agreed to part ways, officially ending his star-crossed tenure in San Francisco.

The Niners issued a statement shortly after Sunday's 20-17 season-ending victory over the Arizona Cardinals, confirming their split with Harbaugh and saying that they already have begun their search for another head coach. Niners CEO Jed York and general manager Trent Baalke will hold a news conference at 1 p.m. PT on Monday.

"Jim and I have come to the conclusion that it is in our mutual best interest to move in different directions," York said in the statement. "We thank Jim for bringing a tremendous competitive nature and a great passion for the game to the 49ers. He and his staff restored a winning culture that has been the standard for our franchise throughout its history. Their commitment and hard work resulted in a period of success that should be looked back on proudly by our organization and our fans. We wish Jim and his family all the best."

"This has been the time of my life, [like] that song," Harbaugh said in a 20-minute news conference following the game but before the parting was announced by the team. "I did. I really did. 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."

Despite the 49ers' overall success during his four-year tenure, Harbaugh's frequent clashes with team management -- specifically Baalke -- fueled speculation about his job security.

Harbaugh's Impact Felt Promptly In his first three coaching jobs, Jim Harbaugh turned pretenders into contenders. Stanford was 1-11 the year before his arrival and four years later he left after an Orange Bowl win. The 49ers went from 6-10 to 13-3 in his first year. 3 yrs prior First 3 years 49ers .438 .760 Stanford .294 .459 << Univ. of San Diego .655 .829 >> 12-1 in 4th season

The Niners went 44-19-1 in their four years under Harbaugh, 49-22-1 including the playoffs.

"I count up these wins," Harbaugh said, "and that's 49 wins, and that seems appropriate. That seems pretty darn good."

Said running back Frank Gore: "I liked how he approached the game of football. My best years, they were with him ... he was here and we won."

Harbaugh has been linked to several coaching vacancies and expected openings in recent months, including the job at the University of Michigan, his alma mater.

Michigan officials, who traveled to the Bay Area to meet with Harbaugh after his final 49ers game, believe they will be taking Harbaugh and his wife to Ann Arbor with them on Monday, sources told ESPN NFL Insider Adam Schefter.

Jim Harbaugh, who went 44-19-1 in his four seasons with the 49ers, had one year remaining on his contract. Jeff Gross/Getty Images

Harbaugh would not specifically address the Michigan stories.

"There will be announcements made concerning those things," Harbaugh said.

The Niners missed the playoffs for the first time under Harbaugh by going 8-8 this season en route to a disappointing third-place finish in the NFC West.

Harbaugh's first three seasons in San Francisco were marked by overwhelming success, as the Niners appeared in the NFC Championship Game three straight times and reached Super Bowl XLVII, in which they were defeated by John Harbaugh's Baltimore Ravens.

But after getting off to a 7-4 start this season, San Francisco struggled down the stretch, losing four of its final five games.