Klaus signed the treaty hours after the constitutional court of the Czech Republic ruled it is in accordance with the country's constitution.
"I have expected the decision by the constitutional court and I respect it although I principally disagree with its contents and reasoning," the president said in a statement.
"I especially cannot agree with the contents of the ruling because the Czech Republic will stop being a sovereign state when the Lisbon Treaty takes effect, despite the political view of the constitutional court," he explained.
The Czech Republic is the remaining one country among the 27 EU members that has not yet ratified it. All countries have to ratify the treaty for it to enter into force, which the union wants by Jan. 1.
With the latest action by the Czech president, the Lisbon Treaty is expected to enter into force on Dec. 1.
For the republic to ratify the treaty, only the signature of President Klaus was missing.
Klaus, a Euro-skeptic, said earlier he would sign the Lisbon Treaty if the Czech Republic is exempt from the treaty's Charter of Fundamental Rights. Last week, EU leaders agreed to accept his demand.