Now with his ruling United People's Freedom Alliance (UPFA) in firm control of parliament, the opposition divided and his main political rival under court martial, his position appears unassailable.
The alliance may have fallen just short of the two-thirds majority that would have allowed Rajapakse to amend the constitution, but with a predicted 140 seats in the 225-member house, it would only need 10 outside votes to make up the required number.
The UPFA secured 117 seats in Thursday's poll and is expected to win at least half of the 45 that have yet to be declared. The main opposition United National Party (UNP) was reduced to 46 seats.
But while the president may have tightened his already formidable grip on power, analysts say he still faces serious challenges in genuinely uniting the Indian Ocean island, especially when it comes to its large Tamil minority.
In his campaigning for the parliamentary election, Rajapakse had asked the electorate to grant him an unequivocal mandate that would put aside political divisions in the pursuit of economic growth after decades of ethnic conflict.
In terms of seats, that mandate was delivered, but on the back of a record low turnout of just 55 percent that raised questions over his claims to have the country behind him.
"This turnout shows people have lost faith in the system," said author and political commentator Victor Ivan.
"The president has a serious challenge before him to restore that confidence and address outstanding political issues," Ivan said.
Previous parliamentary polls have registered average turnouts of around 75 percent, even when voters were faced with the threat of attacks by the Tamil Tiger rebels who routinely attempted to disrupt the electoral process.
The lack of voters this time around was quickly seized upon by the opposition as evidence of widespread dissatisfaction.
"For the first time, we have a parliament which has no mandate from the people," said UNP leader Ranil Wickremesinghe.
The clearest signal of the divisions that remain came from the Tamil minority, which has always been deeply suspicious of Rajapakse's nationalist leanings and also turned out in record low numbers.
The president had campaigned in the Tamil heartland of Jaffna and Wanni with promises of billions of dollars to rebuild the regions worst affected by the long war with the separatist Liberation Tigers of Tamil Eelam (LTTE).
But his party failed to win a single Tamil district, with Tamil voters instead electing 12 MPs from the moderate Tamil National Alliance, which wants greater autonomy for the Tamil minority.
"The results show that Tamils have no confidence in the (majority Sinhalese) government," said human rights campaigner Nimalka Fernando of the National Democratic Council. "The electoral map shows the divisions very clearly."
With his second presidential term secured and a powerful parliamentary majority, Rajapakse would have no excuses for failing to deliver on pledges to address Tamil grievances, Fernando said.
"We have a situation where he can act now," Fernando said. "But it remains to be seen if he will deliver on the promises of peace and national reconciliation."
The Tamils are demanding a genuine devolution of political power, as well as redress for their complaints that discrimination by the Sinhalese majority has deprived them of jobs and education.
"The president's next move will decide the direction of the national (ethnic) question," said Colombo University history lecturer Nirmal Devasiri, who warned that failure to resolve the Tamil issue could lead to fresh ethnic conflict.
Rajapakse's response will also be carefully monitored outside Sri Lanka, with Washington pressing the president to bring the minorities into the political mainstream.
"I think it's important for the administration of President Rajapakse to reach out to the Tamils," US Assistant Secretary of State for South and Central Asia Robert Blake told the BBC in an interview.
"It's important that they feel they're going to be able to live a future of hope and of opportunity," Blake said.