United SC terminated the contract of Baldeep Singh, while East Bengal stood by Jagpreet Singh after both were accused of raping a 14-year-old girl.
The duo and former India international and ex-East Bengal defender Jaspal Parmar are accused of rape.
The police, on Tuesday night, arrested Jagpreet and his cook Ravi Singh while Jaspal and Baldeep are absconding.
A Barrackpore sub-divisional court on Wednesday remanded Jagreet and cook Ravi Singh to 14 days' judicial custody.
"We have terminated Baldeep's contract with immediate effect. Till he's proven innocent, his contract remains null and void," United SC director Nawab Bhattacharya said.
East Bengal, though, contested the rape allegations, saying that Jagpeet was present with the team during their I-League match against Pune FC on Monday afternoon, when the incident is alleged to have taken place.
"Jagpreet was with the team at the stadium. How can he be involved in the incident? These are false allegations. We will not take any action till he's proven guilty. Even the medical report has not yet come," East Bengal general secretary Kalyan Majumdar said.
A former India midfielder, who was with Churchill Brothers last season, Jagpreet joined the club this season but is yet to play a match in the red and gold jersey.
Jaspal Parmar joined East Bengal from Salgaocar, but had asked to be released about two-three weeks back, East Bengal media manager Gautam Roy said.
"Parmar is no more with us. We are not concerned about him," Roy said.
A 14-year-old girl was allegedly raped by four persons, including the three footballers, at their apartment in a north Kolkata high rise.
The girl's father lodged a complaint alleging that four persons raped his daughter at Diamond City North residential complex near Nagerbazar.
Their cook, Ravi Singh, allegedly took the girl to the second-floor flat on Monday afternoon to help in cleaning up.
When the girl returned home on Monday evening, she complained of feeling unwell as she told them of her plight.
The victim's neighbours and relatives rushed to the apartment and beat up the four accused. A team from Dum Dum police station arrested Jagpreet and Ravi.