Having spearheaded the brutal end of the Tamil separatist war a decade ago, Rajapaksa is a divisive figure but popular among his own majority Sinhalese-Buddhist community.
His landslide win split the island nation of 21.6 million on religious and ethnic lines as never before, seven months after deadly Islamist attacks.
Unusually, his inauguration was held at a revered Buddhist shrine with an imposing stupa — reputedly built by a Sinhalese king who vanquished invading Tamils over 2,000 years ago.
At the ceremony, Rajapaksa put his success down to the “extraordinary blessings of the Buddhist monks”.
“The main message of the election is that it was the Sinhala majority vote that allowed me to win the presidency,” the 70-year-old retired lieutenant colonel said.
“I knew that I could win with only the votes of the Sinhala majority. But I asked Tamils and Muslims to be a part of my success. Their response was not what I expected. However, I urge them to join me to build one Sri Lanka,” he said.
Rajapaksa was defence chief under his brother Mahinda’s 2005-15 presidency, when the military conducted a no-holds-barred campaign to end the 37-year war in which 100,000 people perished.
This makes the brothers heroes among Sri Lanka’s Sinhalese majority and the powerful Buddhist clergy.
But around 40,000 Tamil civilians were allegedly killed in the closing stages of the conflict, which ended in 2009, and Saturday’s election saw Tamils — who account for about 15 percent of the population — vote overwhelmingly against Rajapaksa.
As defence secretary Gotabaya had unfettered control over the security forces, while “death squads” that abducted dozens of dissidents, opponents, journalists and others also allegedly reported to him.
Many people were never found again after being bundled into feared white vans, while some were killed and dumped by roadsides.
The new president has denied any involvement and has resisted international calls to investigate the alleged war crimes.
At his only press conference during a three-month election campaign, Rajapaksa reiterated that he will not allow Sri Lankan troops to be tried by any war-crime tribunal, foreign or local.
He had also pledged to exonerate the dozens of military personnel accused of abductions, extortion and killings during his brother’s decade in power.
The island’s Tamils have been campaigning for accountability for war crimes and greater autonomy in areas where Tamils are concentrated.
Tamil youth took up arms in 1972 demanding a separate state and their violent guerilla campaign at its height saw them control a third of the country.
After being in opposition for nearly five years, Rajapaksa announced his intention to run for the presidency just days after Islamist attacks on April 21 that killed 269 people, promising to protect the nation.
The Easter Sunday suicide bombings on three upscale hotels and three churches was carried out by a homegrown outfit from among Sri Lanka’s Muslim minority, who make up 10 percent of the population.
It shocked the nation, and the world, just as Sri Lankan tourism was booming and as the nation prepared to celebrate a decade since the end of the Tamil separatist war.
Rajapakasa insisted that extremists would not have carried out any attacks if he had been in power. He blamed the government of Prime Minister Ranil Wickremesinghe for weakening the intelligence apparatus he had built.