Opposition leader and former parliamentary speaker Delfim Neves was arrested afterwards, and accused by Prime Minister Patrice Trovoada of having staged the attempted putsch.
"All this is just a sham, a show... aimed at physically eliminating people who can be politically troublesome, which includes me," Neves said at a press conference on Wednesday.
Neves was released on bail on Tuesday, his lawyer and STP-Presse said.
Key details about what happened on Friday and the following days remain murky.
Trovoada on Friday said that four people had been arrested after a six-hour gun battle at army headquarters.
Four people had died and the detainees had identified Neves and a mercenary named Arlecio Costa as the "sponsors" of the operation, he said.
The authorities then arrested Neves and Costa, Trovoado said.
But two days later, the armed forces chief of staff said, without elaborating, that three of the four detainees had died of wounds sustained in an "explosion" and Costa had died after he "jumped from a vehicle."
"They killed the living proof" of what had happened, Neves said at the press conference, referring to Costa and the three dead detainees.
"The accuser (the fourth detainee) was left alive to say that Delfim Neves was one of the ringleaders behind this plot," he charged.
He added, "If people hadn't mobilized quickly to get me out of the barracks at 5.30 a.m., Delfim Neves would have been dead the following day as well."
Costa once served in a notorious South African mercenary outfit, the Buffalo Battalion, which was disbanded at the end of apartheid in 1993. He had been previously accused of an attempted coup in Sao Tome in 2009.