Carnesale, who is serving as dean of the Kennedy School as well as provost, took over immediately as acting president.
The most important achievement of Carnesale's 12-week term was the resolution of the University's policy on ROTC.
In an amendment to Rudenstine's November proposal, Carnesale called for the University to cut all financial ties to ROTC while still allowing students to participate.
Carnesale's February 1 amendment was praised by the faculty. It helped secure approval of the plan by the Corporation, the University's more powerful governing board.
"I am especially grateful to Al Carnesale and many others for having kept Harvard steadily moving forward during this time," Rudenstine said in the statement.
Jonathan N. Axelrod contributed to the reporting of this story.