The poll was reduced to a one-horse race earlier in the week when Tsvangirai withdrew complaining of intimidation and violence by supporters of Mugabe's Zanu-PF party.
Ralph Black, the MDC's representative in the United States, told Al Jazeera that a government of national unity may diffuse the current crisis.
"They must agree to form a government of national unity," he said.
"The two parties must come together to select and share power, but we believe Mugabe must not be part of a unity government - this is because the destruction of Zimbabwe's democratic institutions lies squarely at his feet."
Briggs Bomba, a Zimbabwe activist for Africa Action, a non-profit organisation, also told Al Jazeera the strategy the MDC is using has not been effective.
"What the MDC could have done was to mobilise mass popular support inside the country," he said.
"If Zanu-PF supporters, government officials, and the police, saw massive support for the MDC, and saw the people rally in large numbers in support for a change of political direction in the country, they themselves will be forced to re-think their roles as enforcing the policies of Robert Mugabe."
Al Jazeera's Haru Mutasa, reporting from Harare, said that there was better turnout than would be expected in some MDC strongholds, but many of those voting complained of intimidation.
"People who wouldn't really want to talk to you on camera, saying that they were scared, also they would say that, for example, tonight there'll be people going house-to-house checking fingers and if you don't have the red ink to show you voted you could be victimised," she said.
"What is happening today is not an election. It is an exercise in mass intimidation"
Morgan Tsvangirai, opposition leader
"Some people were told the night before, they were gathered round and told to vote for Zanu-PF or there would be ramifications, we're hearing lots of stories."
Paramilitary police in riot gear were deployed in the centre of the capital while youths wearing Zanu-PF t-shirts and bandanas reportedly roamed the streets, singing revolutionary songs, and asking people why they were not voting.
The AFP news agency reported that in some areas of the country, there were allegations that officials were inspecting ballot papers before they were placed in boxes.
Election observers also reported that Zimbabweans were being forced to vote.
"Some of them are saying 'We were told to come here,'" Khalid A. Dahab, spokesman for the Pan African Parliament monitoring team, said. "It's just not normal. There's a lot of tension."
One witness in Chitungwiza town, south of Harare, said Zanu-PF supporters were forcing voters to handover their identity details and the serial number of their ballot paper so they could check how people voted.
The Zimbabwe Crisis Coalition right group said the heads of some rural village leaders had "assisted" teachers to vote after forcing them to declare they were illiterate.
State television denounced 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.
|Tsvangirai remained on the ballot paper despite withdrawing from the election [AFP]
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.
In his last rally before the vote, Mugabe said he would be "magnanimous" in victory.
A spokesman for the Zimbabwe Electoral Commission said that the first results from the 210 constituencies were not expected to be announced until Saturday.
Tsvangirai 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.
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.