A teary-eyed Bob Bowlsby walked out of a Stanford auditorium to a roaring ovation from university coaches and staff members Thursday, leaving behind a lasting legacy at one of the nation’s top athletic programs for a conference in desperate need of a strong leader.

The Big 12 Conference made it official in the afternoon, announcing Bowlsby as its commissioner. He will take over for interim Commissioner Chuck Neinas — who replaced the ousted Dan Beebe in September — on June 15 after six years as Stanford’s athletic director.

“The institutions of the Big 12 wanted a commissioner that could take us to the next era as a conference,” said Burns Hargis, president of Oklahoma State and chairman of the conference’s board of directors. “The search committee looked for a candidate that has a vision for the next generation of college athletics, and his credentials and ideas exceeded this.”

Bowlsby will lead a BCS conference that seems to have found some stability.

After losing four schools over the past two years, the league heads into this fall with 10 members, including new additions TCU and West Virginia. The conference also is working on a new television deal that could reshape revenue similar to the Pac-12’s lucrative contract.

“Bob has been a great friend and confidant,” Pac-12 Commissioner Larry Scott said. “I’ve very much enjoyed working with him and value his tremendous experience, intellect and integrity. I’m sorry we will lose him from Stanford, but I am happy for him and believe he will do a terrific job for the Big 12.”

The 60-year-old Bowlsby had passed up several chances to leave Stanford over the years. He’s a nationally respected college administrator who was hired away from Iowa in 2006 after 15 years spent running the Hawkeyes’ athletic department.

“I have been honored to have served Stanford University. It has been a productive and an enjoyable period of time and Stanford will always be a part of me,” Bowlsby said in a statement. “The university has a rich history of successfully merging world-class academics and world-class athletics and I am very proud to have had the opportunity to participate in the extraordinary achievements of our student-athletes and coaches.”

Success on The Farm blossomed during Bowlsby’s tenure.

Of all the decisions he made at Stanford, though, fans will forever remember his hiring of coach Jim Harbaugh in 2006 most. Harbaugh built the football program into a national power, winning the Orange Bowl over Virginia Tech in 2011 and finishing fourth in the final AP poll.

It was the program’s best ranking since the unbeaten 1940 team finished second.

Bowlsby also hired offensive coordinator David Shaw last year to replace Harbaugh, who departed to the San Francisco 49ers. Shaw kept the Cardinal on track, going 11-2, including an overtime loss in the Fiesta Bowl to Oklahoma State. Andrew Luck was the Heisman Trophy runner-up both seasons.

“Bob Bowlsby has my admiration as a Stanford alumnus for his leadership through difficult economic times for our athletic department,” Shaw said. “As head football coach, he has my gratitude for his continuous efforts to bolster and support our football program. As a friend, I wish him great success.”

Stanford’s rigorous academic standards presented unique circumstances, yet the school has won the Directors’ Cup 17 straight years. The award is given annually by the National Association of Collegiate Directors of Athletics to the program with the most success in all sports.

Stanford is one of the country’s largest programs with 35 sports, including 19 for women. Stanford sent more athletes to the 2008 Beijing Olympics than any other college in the U.S, winning 25 Olympic medals. If Stanford were a country, it would have ranked 11th — tying with Japan — in total medals.

Stanford teams won 10 NCAA championships during his tenure, including five straight Final Four appearances by the women’s basketball teams.

“I am very sad to see Bob leave Stanford. I loved working for Bob. He is a great supporter of women’s basketball and women’s athletics here at Stanford,” said Hall of Fame women’s basketball coach Tara VanDerveer. “He is direct, a problem-solver, and a man of integrity. The Big 12 is fortunate to have him and he will do a great job.”

Bigger challenges lie ahead for Bowlsby in the Midwest.

The Big 12 was hit hard two years ago and wound up losing Nebraska to the Big Ten, Colorado to the Pac-12 and, as of July 1, Texas A&M and Missouri to the Southeastern Conference. Beebe was booted in September as Oklahoma, Texas and others were flirting with the Pac-12 and the Big 12 seemed on the brink of falling apart.

The conference is reportedly working toward a new television deal with ESPN, and Neinas was pushing members to agree to a long-term grant of media rights to the league that would make it all but impossible for schools to bolt. No deal has been struck yet, but that will likely be among the first items on the agenda for Bowlsby.

That’s something he worked closely with Scott to accomplish.

After reaching a 12-year contract worth about $3 billion last year with Fox and ESPN, the Pac-12 announced plans to launch a new conference-owned network to supplement coverage and create more exposure for Pac-12 athletes. The venture will launch this fall with the national cable network, six regional networks and a digital network.

“We’re grateful to Bob Bowlsby for his leadership of Stanford Athletics over the past six years,” Stanford Provost and acting President John Etchemendy said in a statement. “We’re sorry to see him go, but this is a tremendous opportunity for him, and we wish him and the Big 12 all the best.”