"The passport has been returned for all of them, but no reason has been given as to why they had been taken," the official, speaking on condition of anonymity, said.
Tsvangirai, his party's secretary general Tendai Biti, and the opposition's international relations secretary, Eliphas Mukonoweshuro, had had their passports seized when they sought to fly to the regional summit in South Africa, the party had said.
Biti said the incident should send a strong message to leaders of the SADC, a regional bloc bringing together 14 countries, including Zimbabwe.
"We have been trying to tell President [Thabo] Mbeki about things like this, and people wouldn't believe us. But now here it is ... for all to see," he said.
Tsvangirai said he had been invited to attend the weekend SADC summit to be hosted by Mbeki, the South African president, mediating power-sharing talks between Zimbabwe's opposition and Robert Mugabe, Zimbabwe's president.
The talks stalled this week after Mugabe and Tsvangirai failed to agree on senior leadership posts, a sensitive issue for the long-time political rivals.
Tsvangirai has been using emergency travel documents after the authorities refused in June to renew his passport after it expired.
Thursday's incident is likely to raise tensions between Mugabe and Tsvangirai and embarrass Mbeki, who has dismissed criticism that he is too soft on Zimbabwe's president, saying pressure will only aggravate the country's problems.
The political stalemate has worsened an already dire economic crisis. Zimbabwe has the world's highest inflation rate, 80 per cent unemployment and widespread shortages of basic goods.
Tsvangirai told reporters earlier at the airport he was sure power-sharing talks with Mugabe's government would resume.
Asked by reporters if he was still optimistic about a deal, he said: "Oh, yes, of course, we got our independence after how many talks? Hundreds and tens of meetings had been held."
The talks on power-sharing began last month after Mugabe's unopposed re-election in a vote in June that was condemned around the world and boycotted by Tsvangirai because of attacks on his supporters.
Tsvangirai has said Zimbabwe's post-election government should be based on the March 29 first-round presidential election - which he won, but not by a clear majority.
Mugabe says the MDC should accept the result of the June 27 run-off.
"I am there [at the talks] to protect the will of the people and we are taking a principled stand," Tsvangirai said on Thursday.
Arthur Mutambara, whose breakaway MDC faction has 10 seats in parliament, has agreed to power-sharing with Mugabe.