Pilbeam will take office on Sept. 1 and succeed Benedict H. Gross '71, who said in June that he would step down after five years of leading the College.
Smith wrote in a letter to College affiliates that he was "quite pleased" to have Pilbeam lead the College.
"His selflessness and dedication to Harvard are clearly without bounds," Smith wrote.
Smith wrote that he would soon appoint student and faculty committees to advise him as he begins a search for a permanent leader for the College.
Pilbeam, a professor of human evolution and senior adviser to Smith, has said he is not a candidate for the permanent post, Smith wrote in his letter.
In his 26 years as a Harvard professor, Pilbeam has held a number of leadership positions. In April, Pilbeam was summoned to serve as interim dean of the faculty after Jeremy R. Knowles stepped down from his post due to complications from prostate cancer.
Pilbeam was a senior adviser to Gross during the 2006-2007 academic year and a member of the committee tasked with drafting a replacement for the Core Curriculum. He ended his interim stint as Faculty of Arts and Sciences dean on July 15.
Peter T. Ellison, the former dean of the Graduate School of Arts and Sciences and a fellow anthropologist, said in April that because of Pilbeam's previous leadership roles, he would face "no learning curve" in leading the faculty.
"He has remarkable breadth of experience here in the University," Ellison said at the time. "David is skillful and insightful and patient and very quiet in his style. I think many people may not realize what an important role he has played in the Faculty of Arts and Sciences for quite a long time."
Pilbeam's career at Harvard began in 1981 when he became the curator of paleoanthropology at Peabody Museum, a position he still holds today in addition to his professorship.
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—Staff writer Paras D. Bhayani can be reached at email@example.com.