Rakhmonov, who became head of state in 1992, has been criticised by opponents for undermining civil rights, jailing dissidents and allowing only a token opposition.
Opposition parties boycotted Monday's presidential election, saying it was not democratic.
But Rakhmonov's victory margin seemed modest compared to 1999 when he won with 96.4 per cent of the votes.
The Organisation for Security and Cooperation in Europe (OSCE) has criticised the election, saying it was marred by serious irregularities.
"The lack of any serious campaign and credible alternatives undermined this election", Kimmo Kiljunen, the coordinator of a 170-strong OSCE observer mission to Tajikistan, said.
"Observers noted serious shortcomings during polling including widespread family voting, proxy voting, multiple voting and identical signatures on voter lists," he added.
The Central Asian country has never held an election which monitors have judged to be free and fair.
Rakhmonov's four rivals for the presidency were obscure officials from state-friendly parties.
As he cast his ballot, Rakhmonov defended the vote against criticisms of its fairness.
"Tajikistan is a country populated 99 per cent by Muslims and it's a completely different culture and that has to be taken into account," he said.
Rakhmonov got 76.4 per cent of
voter' support in the election
"Do you think it democratic when there is some kind of revolution, blood, or destabilisation? Is that democracy? Absolutely not," he added, alluding to instability in other countries of the former Soviet Union.
Rakhmonov barely campaigned before the election and none of the other four candidates directly criticised him or his policies.
Olimzhon Boboyev of the Economic Reform party came a distant second with 7.2 per cent of the votes. Turnout was 91 per cent.
The leader of the opposition Social Democratic party, one of the groups that boycotted the poll because it disagreed with changes to the constitution which allowed Rakhmonov to stand for a third term and potentially another in seven years time, condemned the vote.
"If the existing president wins there's no point expecting democratic progress," Rakhmatullo Zoirov, the party chairman, told AFP news agency before the results.
A number of potential challengers for the presidency have been jailed over the years, and on Saturday police arrested three opposition activists.
Amid heightened security around the election, police detained six members of the Islamic group Hizb ut-Tahrir, one of whom, a 23-year-old student, was distributing leaflets that declared it sinful to take part in the vote, an interior ministry spokesman said.
Tajikistan was wrecked by a civil war in the early 1990s in which more than 100,000 people died. The war was won by Rakhmonov's Russian-backed forces.
The West has been keen to foster ties with the country since neighbouring Uzbekistan ejected US forces from a base there last year and shut down US-backed non-governmental organisations.