However, Salvador Sanchez Ceren’s rival has the right to appeal and officials say a final declaration cannot yet be made.
Conservative candidate Norman Quijano had earlier called for a new poll after preliminary results indicated a margin of victory of fewer than 7,000 votes.
Salvador Sanchez Ceren would be the first ex-rebel to serve as El Salvador’s president.
He became vice president of El Salvador in 2009, while Norman Quijano was the mayor of the capital, San Salvador.
The election body has already rejected calls from Norman Quijano’s party for a rerun.
The Supreme Electoral Tribunal announced on Thursday that Salvador Sanchez Ceren, a member of the Farabundo Marti Liberation Front (FMLN), had won 50.11% of the vote after a manual count.
Norman Quijano, of the conservative Arena party, won 49.89%, the election body said.
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