Official results give the opposition coalition, the LDS, fifteen seats in the new National Assembly, five more than the People's Party of President James Michel.
Before the result was announced, Mr Michel promised to work with the new assembly.
The opposition had been expected to win the election.
"My hope is that this spirit of consultation continues in the new National Assembly, where we all work together for the common good of our nation," he said.
Does Seychelles live up to its idyllic image?
The LDS (Seychelles Democratic Alliance) consists of the main opposition party, the liberal SNP (Seychelles National Party)  and four smaller opposition parties.
The SNP had refused to take part in the 2011 elections claiming they would not be fair.
Mr Michel's People's Party has been in power ever since the return of multi-party democracy in 1991, and before that during almost 16 years of one-party rule.
The opposition in the Seychelles has won parliamentary elections for the first time in four decades.