Abe defeated former Defense Minister Shigeru Ishiba 108-89 in a runoff vote, The Japan Times reported.
Thanking members of the party for their support, Abe acknowledged his decision to resign abruptly in 2007 caused the LDP major problems. He was suffering from ulcerative colitis at the time, which he says has been cured.
"You have given me a mission to build a new and strong LDP and to stand at the party's helm in these difficult times," he said. "This victory does not erase the responsibility I bear from five years ago but I keep that firmly in mind and will devote myself to seizing government power with everyone."
The party governed Japan almost continuously between 1955, when the Liberal and Japan Democratic parties merged, until 2009, when it was trounced in the most recent national election. Since then, many of its members have left to join existing parties or to help start new ones.
The LDP has been the most conservative of major political groups in Japan, backing free-market economics and the preservation of traditional Japanese culture, including the monarchy.