The men were denied bail in Madhya Pradesh state after appearing in court where they were charged with sedition.
They were arrested after their Hindu neighbours complained that they had burst firecrackers and shouted "pro-Pakistan" slogans during the game.
Pakistan won the final, defeating India by 180 runs.
Sedition is one of the most serious charges under the Indian penal code.
People charged with sedition have to surrender their passports, are not eligible for government jobs, must appear in court as and when required, and spend money on legal fees.
The India Today website quoted police as saying that the men were charged because of the anti-India slogans and not because they were cheering for Pakistan.
Why India needs to get rid of its sedition law
This is not the first time Indian Muslims have got into trouble for cheering for the Pakistan cricket team.
In 2014, 66 Muslim students from Indian-administered Kashmir were kicked out of their university in the northern state of Uttar Pradesh and charged with disturbing communal harmony.
And in 2016, police were sent into a university in Indian-administered Kashmir after clashes between students from the state and other parts of the country.
Fifteen Muslim men have been arrested in India for allegedly shouting "anti-India and pro-Pakistan" slogans during the Champions Trophy cricket final.