The single-candidate presidential election featured Abdu Rabu Mansour Hadi, who served as Saleh's vice president. He is now posed to assume the reins of power in the Arabian Peninsula's poorest nation.
Violence marred voting in the south, where a separatist movement opposed the balloting. At least nine people were reported killed nationwide and balloting was halted in some areas.
But many Yemeni analysts called the vote a success, saying it provided a possible path out of the political crisis that has gripped the nation of 24 million for more than a year. The election was part of a transition plan, worked out by Persian Gulf states, that includes a new constitution and multiparty elections in two years.
"Elections are the only exit route from the crisis which has buffeted Yemen for the past year," Hadi, Yemen's presumptive new leader, reportedly said after voting.
Initial reaction from the U.S. and other nations seemed positive.
"We congratulate the Yemenis for really launching this process, taking ownership of it as a population, and we will stand with them as they take the next steps," Victoria Nuland, U.S. State Department spokeswoman, said in Washington.
Saleh, who finally agreed to step down after protracted negotiations, becomes the fourth Arab strongman to lose power amid popular protests, following the former leaders of Tunisia, Egypt and Libya. He remains in the United States for medical treatment of burns suffered in an assassination attempt last year.
Yemenis voted with their thumbs, placing them in ink and then stamping their prints on ballots bearing a picture of Hadi and a map of Yemen. Some estimates put turnout at 80%. Final results won't be known for several days.
But some Yemenis refused to vote, voicing displeasure with the rubber-stamp nature of the election and the fact that a close confidant of Saleh was the only candidate.
Yemen faces daunting challenges, including widespread poverty, a separatist threat in the south, a rebellion in the north and the presence in the country of Al Qaeda militants.
Al-Alayaa is a special correspondent. Times staff writer Patrick J. McDonnell in Beirut contributed to this report.