However, more than 77 per cent of Jaffna's voters stayed away from the ballot and only half of the Vavuniya voters cast their votes.
"We have undergone a lot of hardship but we have no solutions to our problems. So we are in no mood to vote. It's not going to make any difference," G. Selvam, a 52-year-old Jaffna resident, said.
Al Jazeera's David Chater, reporting from the capital, Colombo, said that the success of the Tamil National Alliance in Vavuniya had been a surprise to many people.
"Certainly we are seeing a result that was unexpected and certainly will be unwelcome for the government," he said.
"In the end it is the beginning of a process, the beginning of the healing, that can mean that the island can try to reunite, but with more than 250,000 displaced Tamils inside the camps the Tamil people have not really been given a full voice by these elections.
"There are still very open wounds in this society, but it is welcome the fact that there is a democratic election, even though now journalists have been allowed to watch it."
Suresh Premachandran, a member of the Tamil National Alliance - seen as having close links with the rebels - said the elections were just a government show.
"The Tamil people do not want an election at this time when hundreds of thousands of their relatives are held in government camps," he said.
President Rajapaksa promised Sri Lanka's minority Tamils more democracy after defeating the LTTE, who fought to create a separate nation for Tamils to free them from what they said were abuses by governments led by the Sinhalese majority.
Riding a wave of popularity since winning the war, Rajapaksa is expected to hold early parliamentary and government elections to secure himself another six-year term.
The shadow of the war, which ended less than three months ago, hung over the polls on Saturday, with 250,000 Tamils who fled fighting still languishing in tightly guarded refugee camps
Ruling party candidates included government allies who ran paramilitary groups that operated as army proxies to fight the LTTE.
"The people who are contesting in the elections are the same people who shot us and abducted our people," one resident of Chundikkuli, near Jaffna, said.
"I don't think the election results will help us in anyway, so I abstained from voting," the resident said.