Businessman Manuel Baldizon had been tipped to win but trailed in with 19.3%, slightly ahead of former first lady Sandra Torres on 17.9
President Perez Molina resigns
The incumbent president was toppled by a corruption scandal last week.
Otto Perez resigned on Thursday and has spent the weekend in jail pending possible charges.
The lack of a clear result will prolong the political uncertainty, said by some to be the worst in the Central American country in two decades.
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