The players who held a three-week strike in 2002 which halted the championship had threatened to stop work again over their claims that some first and second division clubs owed them a total of nearly $1million in unpaid wages and bonuses.
'All we wanted was for them to pay the wages and bonuses' Carlos Soto president of the players' union SIFUP told reporters.
The clubs reached their agreement on Wednesday evening at a meeting of the Chilean football league (ANFP). They also agreed that any of their members who did not keep to the agreement could be thrown out of the league - a move which even surprised SIFUP.
'We never thought the clubs who have respected the agreement would vote to throw out the ones who didn't' said Soto.
SIFUP said the debtors included first division Puerto Montt Deportes Concepcion Temuco Everton Santiago and Union San Felipe.
Some of the smaller clubs said the measures were unfair.
'We've done everything the right way and our debts are the results of administrations from before 2000' said Deportes Concepcion president Luis Morales.
'If it wasn't for the old debts we'd be making a profit.'
Strikes have become common all over South America where professional clubs have chronic financial difficulties and in the last few years have also hit Argentina Peru and Uruguay.