Mr Saleh won 82 percent of the vote while his main opponent, former oil minister Faisal bin Shamlan, garnered 16 percent, the head of the high electoral commission Abdelwahab al-Charif announced late on Wednesday.
"These figures do not represent the final results," he added.
Yemenis went to the polls amid security concerns after the arrest of an al-Qaeda suspect authorities said was planning attacks on the capital.
Five people were killed and six wounded in clashes between the veteran incumbent's supporters and those of the opposition, prompting voting to be suspended in about a dozen of the nation's 5,620 polling stations.
Yemeni television showed long queues of voters even before polling stations opened in the five-way presidential ballot, which was held simultaneously with municipal elections.
Nearly 90,000 troops and police were deployed to oversee voting by the 9.25 million eligible electors, 3.9 million of them women.
As voting was underway, a security official said a suspected member of al-Qaeda was caught in the capital armed with explosives.
"According to the early results of the investigation, the suspect had planned several terrorist attacks in the capital," he told news agency AFP.
Women voters in the conservative Arabian peninsula republic turned up clothed from head to toe in black. They formed separate queues and were searched by policewomen as they entered the polling booths.
"Today is a real celebration of Yemen's democracy as we set the foundations for Yemen's future in (a way which allows) peaceful alternation of power," President Saleh said as he cast his ballot.
President Saleh, who first took office as leader of the then North Yemen in 1978, has survived a 1994 civil war with the former communist south, and al-Qaeda-inspired violence in Osama bin Laden's ancestral homeland, but now faces a challenger at the ballot box backed by both Islamists and former communists.
The 64-year-old father of seven, of the ruling General People's Congress, is being taken on by the 72-year-old Mr bin Shamlan in a test of Washington's efforts to export democracy to the Middle East.
On the eve of polling day, Mr Saleh had announced the arrest of an al-Qaeda-linked "terrorist" in bin Shamlan's entourage on suspicion of plotting attacks on US interests.
But the challenger's supporters retorted that the man detained had worked for just seven days as a bodyguard before being dismissed as a suspected government agent.
Washington said it was in favour of free and fair elections but denied it had foisted them on Yemen.
"The United States as a friendly country has been suggesting it, our advice has been directed at the need for a proper contest," US embassy number two Nabil Khoury told AFP. "But it's something the Yemeni people have been calling for."