Final results of parliamentary elections showed Rajapakse's United People's Freedom Alliance had secured 144 seats in the 225-member assembly in the April 8 vote.
The final result was delayed due to a poll re-run on Tuesday in two constituencies where violence disrupted initial voting.
The results left Rajapakse just short of the two-thirds majority required for the government to rewrite the constitution, which at present prevents him from standing again when his second term ends in 2016.
Attention now turns to the opening of the new parliament on Thursday, which opposition leader Fonseka, who is under military arrest and standing trial at a court martial, is due to attend.
Fonseka is to be allowed to attend parliamentary sessions before being returned to detention after each session, government officials said.
Political observers believe Fonseka is likely to use his position in parliament to attack the president and air allegations of human rights abuses plaguing the gov