But with more than 90% of the votes counted, PM Yulia Tymoshenko has closed the gap to 2.2% on her rival.
Mr Yanukovych called on Mrs Tymoshenko to quit, but she refused and is expected to challenge the result.
The results suggest a remarkable comeback after Mr Yanukovych was swept aside by the 2004 "Orange Revolution".
Under the 59-year-old former mechanic, Ukraine's foreign policy is expected to become more pro-Russian.
'Full circle'
The BBC's Richard Galpin in Kiev says a Yanukovych win would be an extraordinary indictment of the pro-Western Orange Revolution leaders' failure to deliver on their promises, which has left people deeply disillusioned.
Politics in Ukraine has now gone full circle, our correspondent adds.
Mr Yanukovych was a presidential candidate in the last election in 2004, which was found to have been rigged in his favour.
Mrs Tymoshenko's impassioned leadership of the subsequent street protests that swept him from power - and thrust her to office, along with Viktor Yushchenko - made her an international celebrity.
Incumbent President Viktor Yushchenko lost in the first round of the election last month.
With more than 94% of votes counted, Ukraine's electoral commission put Mr Yanukovych ahead with some 48.3% of the vote, ahead of Mrs Tymoshenko at around 46.1%.
If confirmed, it would be a narrower margin of victory than Mr Yanukovych had been hoping for.
Mr Yanukovych has already congratulated his supporters and said he will deliver the change the country is yearning for.
He reportedly said it was time for his rival to quit.
"I think that Yulia Tymoshenko should prepare to resign. She understands that well," Interfax-Ukraine quoted him as saying in a television interview.
"In any case, I believe such a suggestion will be put to her."
But Mrs Tymoshenko, 49, showed no sign of standing down.
In a news conference, she said her team was conducting a "parallel count" and urged them to "fight for every result, every document, every vote", reports Reuters news agency.
The election commission is not due to release preliminary results until Monday morning, but our correspondent in Ukraine says exit polls there are generally accurate.
Mud-slinging
Mr Yanukovych won last month's first round of voting, finishing 10 percentage points ahead of Mrs Tymoshenko.
She has threatened to take her supporters to the streets if defeated, saying the protests could be larger than those of the Orange Revolution.
Sunday's vote came after a bitter mud-slinging campaign in which real policy issues and debate appeared to have been forgotten, says our correspondent.
On Saturday, Mrs Tymoshenko's political bloc accused Mr Yanukovych's Party of Regions of blocking her supporters from overseeing the vote in the eastern Donetsk region.
Mr Yanukovych's camp hit back with allegations that some supporters of the prime minister had been tampering with ballots in an attempt to get votes from eastern Ukraine disqualified.
President Yushchenko - who came fifth in last month's first round - led a series of bitter personal attacks on former ally Mrs Tymoshenko during the campaign.
His working relationship with the prime minister over the last five years was poisoned by bickering as Ukraine became engulfed by an economic crisis, with its GDP plummeted 15% last year.
