It was set to be a big fight between the ex-rebel and the gang-buster, but in the end it was an indecisive scrap that will send voters back to the polls for a run-off in March.
I watched a big screen at polling headquarters as the number of votes for the socialist FMLN candidate, Salvador Sanchez Ceren, crept towards the magic 50% mark, only to hover and get stuck in the end.
"It means the FMLN party will win in the run-off," Luis Membreno, talk show host and economist, told me, pointing out that the FMLN had a 10-point lead over its rivals ARENA.
"ARENA will need to find 250,000 new voters to close the gap before March 9, and that's close to impossible."
That could mean this was an incomplete victory for the FMLN over their right-wing rivals, but at San Salvador's forensic laboratories, they are too busy to pay much attention.
Here, in cramped offices, scientists are surrounded by boxes of human bones, skulls with holes in them, and a constant need for surgical masks to guard against the stench of death.
Their workspaces are a testament to a faltering and fragile truce between the MS-13 and 18th Street gangs that have been the pivotal issue for voters.
Norman Quijano, ARENA's candidate and former mayor of San Salvador, has promised to bring in the armed forces to fix the problem. Critics say such a move would cause a bloodbath.
The FMLN party managed to put a truce in place that, according to official figures, has drastically reduced murders but there is growing evidence that the truce is slowly collapsing.
Days before Sunday's vote, scientists at the labs were ordered to stop fresh investigations.
According to the attorney-general' office, it was a matter of reverting resources to the election but the lab's lead doctor believes it is political subterfuge and a way of keeping awkward statistics down.
"We have no political colour. We are interested in scientific truth," Dr Jose Miguel Fortin Magana, the lab's director, says.
"Unfortunately politicians seem to be only interested in votes, more than anything else, and that’s why we are unable to continue our work."
For Quijano and Sanchez then its back to the campaign trial and a fight to the bitter end.
But whoever becomes El Salvador's next president will have a tough road ahead.
The economy is stagnant, too many people live below the poverty line and El Salvador's gangs may be a problem too big for either candidate.