Club vice-president Jose Manuel Lopez and team captain Alexis Henriquez issued a joint statement announcing the agreement ending two days of strike action by the players.
"The club will gradually pay with gate takings the salaries of the players who are lifting the strike and have committed themselves to improving their performances in search of better sporting and economic results," they said.
"The club's directors also committed themselves to carry on seeking resources from sponsorship, takings and advertising to get up to date with all payments."
The board of Manizales-based Caldas, crowned South American champions in 2004, had sought Labour ministry support on Tuesday to end the strike by 19 of their players.
Henriquez, quoted by the daily El Espectador on Tuesday, said: "We decided to strike because... most of us can't pay for food, our utilities have been cut and our kids are being sent home from school."
A recent strike threat by players of America, one of Colombia's biggest and most successful clubs, met with partial success when part of their back salaries was paid.
However, their coach Jorge Bermudez, a former Boca Juniors and Colombia defender, was sacked for backing the players.
