In a brief statement the club also confirmed that midfielder Marco Hoger has been suspended from training and first team action for the next week.
Boateng joined the Gelsenkirchen club from AC Milan for 15m euros in August 2013 and still had more than a year to run on his contract.
Sam arrived from Bayer Leverkusen last summer on a contract until 2018 but has struggled to make an impact, failing to find the net in 14 appearances for the club.
The loss to Koln was described by Schalke midfielder Julian Draxler one the side???s ???worst performances in recent years??? and sporting director Horst Heldt announced there would be consequences.
Schalke are now 13 points behind fourth-placed Bayer Leverkusen and in danger of missing out on European football next season after losing to a side who secured their safety thanks to the three points.
Boateng and Sam appear to be the first to pay the price for a disappointing season at the Veltins-Arena.