His departure is a historic moment for the island nation of 22 million, which the Rajapaksas had ruled with an iron fist for much of the past two decades before losing the faith of their once adoring citizens.
"The sight of Gotabaya Rajapaksa fleeing Sri lanka on an air force plane represents (the downfall) of this family," said Ganeshan Wignaraja, senior research associate at the British think tank, ODI Global.
"Their legacy I don't think is a positive one. But one hopes that Sri Lanka will move on in a new direction."
With jubilant Sri Lankans still swimming in the presidential pool, singing in the presidential dining room and dancing around the opulent presidential grounds, it is clear many share that optimism -- at least for now.
What happens during the next 24 hours will do much to determine the country's future, with Rajapaksa's long-term intentions remaining as yet unclear.
The rise of the Rajapaksas
As the country takes its first steps in its brave new era, experts say it would do well to consider what went wrong with the last one -- starting with the rise and fall of the Rajapaksas.
That victory gave Mahinda Rajapaksa an almost inexhaustible well of political capital to draw on and he would go on to enjoy a 10-year grip on power during which he was venerated by Sri Lanka's Sinhalese Buddhist majority. He was popularly referred to as "appachchi" -- the father of the nation -- and people would often bow when he walked past and fear for him when he was unwell.
For much of his term, Mahinda Rajapaksa ran Sri Lanka like a family business, appointing his brothers to key positions; Gotabaya as Defense Secretary, Basil as Minister of Economic Development, and Chamal as the Speaker of Parliament.
And while the good times were rolling, despite gripes about nepotism, the brothers remained popular. The country saw years of growth, fueled by the government's vast borrowing from overseas to fund public services.
But the good times weren't to last.
Brief hiatus and comeback
While the civil war did much to create Mahinda Rajapaksa's legend, it also contained the first signs of his downfall.
Mahinda Rajapaksa's government has always vehemently denied such allegations.
However, its problems began to mount.
At the same time, anger at Mahinda's perceived cronyism grew as signs of economic trouble emerged and it became clear that there would be a price to pay for the government's earlier largesse.
"Sri Lanka is a democratic country and people were shocked at that extent of attempting cronyism," Wignaraja said. "This combination of (nepotism) and mismanaging the economy... people were upset they elected these people."
That might have been enough to finish off a lesser dynasty, but not the Rajapaksas.
In November of that year, Gotabaya Rajapaksa was elected as the country's new President. And like his brother, he saw governing as a family affair.
"People have once again imposed their full confidence in us," Mahinda Rajapaksa said after a landslide victory in parliamentary elections a year later.
"We will fulfill their aspirations and will always value the confidence they have placed in us."
Gotabaya appointed Mahinda Rajapaksa shortly after.
'Fall from grace'
Still, as had happened to his brother, cracks began to emerge in Gotabaya Rajapaksa's presidency as questions over his government's economic management continued to grow.
Murtaza Jafferjee, chair of Colombo-based think tank Advocata Institute, said the vast borrowing spree Sri Lanka embarked on to fund its public service coincided with a series of hammer blows to the Sri Lankan economy, from natural disasters such as heavy monsoons, to man-made ones.
Facing a massive deficit, Rajapaksa slashed taxes in a doomed attempt to stimulate the economy.
But the move backfired, instead hitting government revenue. Ratings agencies then downgraded Sri Lanka to near default levels, meaning the country lost access to overseas markets. Sri Lanka then had to use its foreign exchange reserves to pay off government debt. This affected imports of fuel and other essentials, which sent prices soaring.
And it is the Rajapaksas they blame. For months, angry Sri Lankans have taken to the streets, accusing Gotabaya and Mahinda Rajapaksa of mismanaging the economy.
Those protests began peacefully but turned violent in May, prompting Mahinda Rajapaksa to resign as Prime Minister. But his decision did little to quell frustrations -- and his brother remained in power as the President.
For weeks Gotabaya clung on, apparently unwilling to let the dynasty fall. But ultimately he had no choice, as the lavish home he once used to entertain power brokers was taken over by crowds escaping the heat in his sparkling swimming pool and holding picnics on his sprawling lawn.
As Wignaraja pointed out, the imagery was a fitting end to an era.
"You have this idea that the ruling elite are living very lavishly, while being very corrupt, and the ordinary person is in grave difficulty," Wignaraja said.
"To go from being perceived as heroes, to being chased out of your own home is unthinkable. It's a complete fall from grace."
CNN's Iqbal Athas contributed to this report.