"The board met for two and a half hours, we thought thoroughly about the situation and opted to stay in the competition so as not to be accused of interfering with the integrity of the game," said club president Joao Bartolomeu.
"Leiria will be present at the Luz stadium to play Benfica tomorrow. We will count on youth-team players for the next few matches. We have 14 or 15 players available," he told Portuguese television.
The bottom club are five points from safety with two matches left this season. They lost 4-0 to Feirense last weekend but Bartolomeu hailed the bravery of the eight players who took the field.
"This situation made Leiria's relegation irreversible and it will force the club to withdraw from the Premier League, with all its subsequent consequences," said Leiria in an earlier statement on Friday.
Although Porto have already won the title, Leiria's pullout would have triggered changes in the table and affected the battle for European spots if they had their results this season revoked.
Under that scenario, third-placed Braga's lead over Sporting in fourth spot would have doubled to six points and also lifted them within a point of Benfica.
Last weekend the players' union said 16 Leiria squad members had submitted resignation letters after going several months without pay.
The club said on Friday that only 13 had sent letters.
"The unjustified absence from practice sessions and from the match against Feirense was a violation of the players' duties," said Leiria before adding they had seriously damaged the club's reputation and finances.
"We have the right to demand compensation for all the damage resulting from this situation."
National football federation chief Fernando Gomes said Leiria's proposed pullout would have been "a very bad moment for Portuguese football".
"The salary delay, financial difficulties and the bad image Portuguese football has projected is not at all desirable," Gomes explained.
"What I regret the most is the footballers, their families, the coaches and the club's staff are involved," Gomes said before adding the FPF would do everything to resolve the problem.
Portugal's Professional Football League (LPFP) also said it was studying ways to avoid a repetition and added the country's debt crisis was having a profound impact on the game.