The 49ers went from Jim Harbaugh to “Jim Nobody from Nowhere.”

Four years after making a splash by hiring Harbaugh as their head coach, the 49ers made many of their fans perplexed by replacing him Wednesday with defensive line coach Jim Tomsula, whose self-given “Nowhere” nickname is a nod to his anonymity.

Tomsula, 46, obviously comes with far less fanfare than Harbaugh, the former NFL quarterback who arrived after resurrecting Stanford’s once-pushover program. Tomsula, a defensive lineman at Division II Catawba College, comes to the top job despite never having been an NFL coordinator.

His NFL resume consists of his eight seasons leading the 49ers’ defensive line, although the last of his nine seasons in now-defunct NFL Europe was spent as head coach of the Rhein Fire.

Tomsula, the longest-tenured member of the staff, was the 49ers’ interim coach for the 2010 regular-season finale when he first flashed his colorful everyman persona. In truth, he’s far more than a blue-collar jokester. He is popular among players, but he is also demanding and is regarded as one of the NFL’s best position coaches after tutoring a host of undrafted free agents who have carved out NFL careers.

But his promotion is certain to be met with skepticism. Of the nine candidates considered for the job, Tomsula has the least NFL experience and is the only coach who’s never been a coordinator in the league. It’s not known if the 49ers had a formal interview with Tomsula before making the hire.

A day after parting ways with Harbaugh, 49ers CEO Jed York said he was seeking a teacher in his next head-coaching hire. He also expressed a desire to “win with class,” which was viewed as a shot at Harbaugh, whose strong personality helps explain why he’s now at the University of Michigan. On Wednesday, York hit on both of his previous themes in hailing Tomsula’s hiring.

“After conducting a thorough coaching search, and meeting with a number of outstanding candidates, Jim Tomsula clearly is the right man to lead this team,” York said. “Jim is a great teacher and a tremendous mentor who conducts himself with great class and integrity.”

The in-house hiring evidently wasn’t made to maintain continuity for a franchise that had a 36-11-1 record and reached three straight NFC title games before this season’s disappointing 8-8 record. The 49ers will retain only running backs coach Tom Rathman from its remaining staff, Fox Sports reported Wednesday night. Rathman, the second-longest tenured member of the staff, is close with running back Frank Gore, 31, the franchise’s career rushing leader who is a pending free agent.

The reported exodus of assistants comes as a surprise. However, it was expected that defensive coordinator Vic Fangio, who interviewed for the head-coaching opening, would request to be released from his contract after being passed over. Fangio, 56, is a 28-year NFL veteran with 15 years of experience as a coordinator. He oversaw a defense that allowed the second-fewest points in the NFL over the past four seasons. Raiders defensive coordinator Jason Tarver, 40, would be a candidate to replace Fangio, a source said. Tarver was the 49ers’ outside linebackers coach from 2005 to 2010.

The 49ers clearly identified Tomsula as a favorite from the start, but they also had strong interest in Broncos offensive coordinator Adam Gase, 36.

They conducted their second interview with Gase on Tuesday in the Denver area, but the Broncos also have interest in making him their next head coach. Gase met with Broncos general manager John Elway on Wednesday morning about their head-coaching opening, the Denver Post reported. Gase has worked with the Broncos since 2009.

It's not known if Tomsula’s promotion will sway All-Pro defensive tackle Justin Smith, 35, to return for a 15th season. In December, Smith said he hadn't made up his mind about coming back in 2015, but a source said he would be more inclined to postpone retirement if Tomsula or Fangio was named head coach.

Eric Branch is a San Francisco Chronicle staff writer. E-mail: ebranch@sfchronicle.com Twitter: @Eric_Branch

49ers coaching history

Jim Tomsula

Coaching experience

NFL

49ers: Defensive line coach (2007-14), interim head coach (2010, one game)

NFL EUROPE

Rhein Fire: Head coach (2006)

Berlin Thunder: Defensive coordinator/special teams (2004-05)

Scottish Claymores: Defensive line, special teams, outside linebackers (1999-2003)

England Monarchs: Defensive line, special teams (1998)

COLLEGE

Catawba College: Assistant head coach, defensive coordinator, defensive line, special teams, strength and conditioning (1989, 1997-99, 2001-05)

Charleston Southern: Linebackers, defensive line, strength and conditioning (1992-95)

HIGH SCHOOL

Woodland Hills, Pa.: Defensive line (1990)

Playing experience

Catawba College (1987-88)

Middle Tennessee State (1985)