Sparta coach Jozef Chovanec said: "Patrik told me yesterday, 'It's over. My knee doesn't support the burden anymore'.
"We have to deal with it.
"Thank you Patrik for everything you have done for Sparta and the entire Czech football."
Berger, who also had a loan spell at Stoke during an 11-year spell in England, has not been able to make an appearance for Sparta since August 8.
The Czech international won 44 caps and was a key part of the team which reached the Euro 96 final, where they lost 2-1 to Germany. Berger scored a penalty to put the Czechs in front in the final, before two Oliver Bierhoff goals won the match for Germany.