Rajapaksa, who called the elections two years before his term expires in what analysts say is an attempt to take credit for ending the war, is backed by the United People's Freedom Alliance.
Fonseka, who fell out with Rajapaksa over who was responsible for the victory against the Tigers, has the support of the two main opposition parties, the United National Party (UNP) and the Marxist Janatha Vimukthi Peremuna (JVP).
Those two parties differ on economic policies, but have united behind Fonseka to take on Rajapaksa.
The main Tamil party, which had earlier backed the Tamil Tiger fighters, has not announced who it will support, though analysts say it would probably lean to Fonseka as minorities have more confidence in the UNP.
Tamils make up almost 12 per cent of Sri Lanka's population and, unlike past elections where the Tamil Tigers discouraged them from going to the polls, they could emerge as a key swing vote.
Analysts say whoever wins will need a stable government to carry out reforms.
"If Fonseka wins, he will have a better economic policy as he is backed by the UNP," said Sirimal Abeyratne, a senior economics lecturer at University of Colombo.
"But it depends on his political strength and influence of the JVP. If Rajapaksa wins, he has to undertake some bold reforms to revive the economy, but he needs a strong government."
In the past, governments won national polls on promises to end the war with the Tamil Tigers, or the Liberation Tigers of Tamil Eelam, while blaming the conflict for any failure to implement economic and political reforms.
Sri Lanka's economy, still struggling to recover from both the financial crisis and the civil war, is expected to expand at an eight-year low of 3.5 per cent this year, from six per cent last year, the central bank said.