Criciuma supporters sang "ao, ao, ao, abastece o aviao" (oh oh oh, refuel the plane) in reference to the tragedy, which investigators concluded was caused by fuel exhaustion after the pilots failed to stop and refuel the aircraft en route to Colombia.
Poor planning by the airline and issues with the Bolivian aviation authorities were cited.
There was global mourning over the incident, although Chapecoense revealed recently that the only club to have helped them financially were FC Barcelona of Spain.
Criciuma, who lost the game 1-0, have distanced themselves from the disgraceful conduct of what it describes as a small portion of supporters.
"Criciúma Esporte Clube does not condone and repudiates the chants of fans that took place on Sunday night in the Heriberto Hülse stadium, during the match against the Chapecoense Football Association, in the final round of the Santa Catarina Championship," they said in a statement on Monday night.
"This type of chant from a small number fans does not express the principles of the Criciúma Esporte Clube and its great fanbase, that has enormous respect not only for Chapecoense, but all the clubs in Santa Catarina, Brazil and worldwide
"The song chanted by half a dozen fans is of deeply bad taste and does not match the sporting spirit that guides Criciúma Esporte Clube.
"The images in question will be forwarded to the competent authorities for liability."