The 46-year-old Tomsula has been with the organization since 2007 and has held the top job once before, taking over as interim coach with one game remaining in 2010 after the team fired Mike Singletary. The 49ers won that contest.
San Francisco is the only NFL franchise that Tomsula has worked for after coming over from the Rhein Fire of the now-defunct NFL Europe league.
Niners CEO Jed York said after the team mutually parted ways with Harbaugh that the team was looking for a "teacher." General manager Trent Baalke and the team believe they found that man in Tomsula.
Tomsula ascending to the top gig indicates that respected defensive coordinator Vic Fangio will almost certainly leave the Bay Area. Raiders coordinator Jason Tarver is an option to replace him, per Rapoport.
Tomsula has helped lead one of the best defensive lines in football over the past four years. His unit continued to dominate football games this season despite missing superstar Aldon Smith for nine contests.
The big questions lay on the offensive side of the ball and whom Tomsula will select as his offensive coordinator -- the much-maligned former coordinator Greg Roman signed in Buffalo this week.
The choice will be the new coach's first big decision as that coordinator will be responsible for helping turn around quarterback Colin Kaepernick, who struggled mightily in 2014.
With Tomsula ascending to head coach the 49ers' defense should remain one of the best in the NFL. How the offense changes will be fascinating to watch this offseason.