The polls were triggered by the mass resignation of the leadership of the Malaysian Chinese Association (MCA), the second-largest member of the governing Barisan Nasional (BN) coalition, earlier this month.
More than 100 candidates representing various factions within the party contested for 31 posts.
Deputy president Chua Soi Lek, who was suspended over a sex tape scandal in 2009, won the party election with a slim majority by securing 901 votes.
Chua's sacking had triggered bitter factional fighting.
Incumbent president Ong Tee Keat got 833 votes while former president Ong Ka Ting won 578 votes.
Prime Minister Najib Razak has pressed the party to resolve the crisis, as his coalition attempts to regain the support of minorities -- including ethnic Chinese and Indians -- who dropped the BN in 2008 elections.
"The purpose of (Sunday's) election is to stabilise the party ahead of the next general election, which is likely to be held before the end of this year," said James Chin, a political scientist at Monash University's campus in Kuala Lumpur.
Chin said Chua won because he had "better organisational skills," and the party members realised it was a crucial element for MCA to have him at the helm ahead of the polls.
"The Chinese community are politically matured," he said, in reference to Chua being caught on video having extramarital sex.
After days of intense campaigning, more than 2,300 delegates picked their new leaders.
Chin said the results might ease tensions within the party, but the MCA would not be able to claw back the Chinese support it lost in 2008.
"The party is seen as unable to protect Chinese interest in the ruling coalition. The Barisan Nasional ruling coalition is too dominated by the United Malays National Organisation and Malay interest," he said earlier.
The MCA suffered its worst ever electoral defeat in 2008, winning less than half of the parliamentary and state seats it contested.