A spokesman for the Zimbabwe Electoral Commission said that counting would start immediately but the first results from the 210 constituencies were not expected to be announced until Saturday.
In a statement to party supporters on Friday, Tsvangirai said: "Today is not an election. Today is a shameful humiliation, another tragic day in our nation's history."
"Today's results will be meaningless because they do not reflect the will of the people of Zimbabwe. Today's results reflect only the fear of the people of Zimbabwe.
Mugabe voted with his wife at Highfield Township, on the outskirts of the capital Harare.
Asked how he felt, he told journalists: "Very fit, optimistic, upbeat," before being driven away.
Al Jazeera's Haru Mutasa, reporting from capital Harare, said activity at polling stations, which opened at 7am (5:00 GMT), was much slower than in March's election, and people were being marched down to polling stations, apartment by apartment.
"Today's results will be meaningless because they do not reflect the will of the people of Zimbabwe"
Morgan Tsvangirai, opposition leader
"Generally, those who went to the polling stations said they had to go their for their own safety, because tonight there is a rumour that a 'red finger operation' will take place.
"This means that if you don't have the red ink on your finger, showing that you voted, it will be assumed that you are supporting the MDC and a doubter of Mugabe."
"People are depressed ... Those who wanted to vote genuinely have been scared off. Opposition supporters didn't feel the need to come and vote.
"People would rather spend eight hours in a queue lining up for bread, than they would eight hours in a queue lining up for vote," she said.
Nelson Chamisa, the MDC spokesman, had earlier said that Mugabe's supporters would force people to vote and could attack those that chose not to go to the polls.
"Last night people spent the whole night at vigils, where they were being indoctrinated, threatened with war if they were not going to vote," he said.
"Mugabe has lost support, so as legitimacy decreases, force would increase, as his popularity goes down, he is going to be violent and desperate, that's why you have seen his last kicks, they are very dangerous."
Marwick Khumalo, head of election monitors from the Pan African Parliament, said:"There is no doubt turnout will be very low."
Abel Chikomo of the independent Zimbabwe Media Monitoring Project in Bulawayo told the Associated Press news agency: "There are more queues at bars than at polling stations. People know the election is a farce."
But state television denounced foreign media reports of low turnout, showing long queues in a semi-rural constituency close to Harare and saying that voters had ignored MDC appeals to abstain.
In his last rally before the vote, Mugabe said he would be "magnanimous" in victory.
"Should we emerge victorious, which I believe we will, sure we won't be arrogant, we will be magnanimous and say 'let's sit down and talk,' and talk we shall," Mugabe told a rally on the outskirts of Harare on Thursday.
|Mugabe told supporters that he would be "magnanimous" in victory [AFP]
"So there it is, let the MDC reject it or accept it. We will continue to rule this country in the way we believe it should be ruled."
Tsvangirai on Friday urged other countries not to recognise the results of the run-off.
"Anyone who recognises the result of this election is denying the will of the Zimbabwean people and standing in the way of a transition that will deliver peace and prosperity, not just to Zimbabwe, but the whole region," he said.
Mike Mulongoti, Zambia's minister for information, condemned Mugabe's government for their conduct during campaigning.
"When we tell our neighbours that we'll help them fight for independence [from white-minority rule, as Zambia did during the 1960s and 1970s], we did not agree to bring in a black oppressor after removing a white oppressor," he told Al Jazeera.
"If we knew this would be the case, we would have not appeared in the liberation wars."
Tsvangirai's withdrawal had been followed by international calls for the 84-year-old president not to go ahead with the election unopposed.
Condoleezza Rice, the US secretary of state, warned Mugabe that were he to declare himself the victor on Friday the result would be seen as "illegitimate".
While leaders of the Southern African Development Community (SADC) said that the election should be delayed while Mugabe's government and the MDC hold talks.
However, Bright Matonga, Zimbabwe's deputy information minister, told Al Jazeera that there was no need for negotiations as Zimbabweans would make their choice at the ballot box.
The MDC says that at least 80 of its supporters have been killed by Zanu-PF loyalists and another 200,000 people have been displaced in what it calls Mugabe's "campaign of intimidation" to deter people from voting.
Mugabe supporters have denied the allegations.