Since Article I is the only Article with 9 sections, and since Article I, Section 9 does include some basic protections of civil liberties, I have edited your question to specify Article I.
This section of the Constitution protects civil liberties in three ways. They are:
- Guarantee of the right to habeas corpus. This ensures the government cannot hold a person indefinitely without charging them with a crime.
- Ban on bills of attainder. These are laws passed by a legislature declaring some person or group of people guilty of a crime. The ban prevented the Congress from doing this, thus bypassing the courts.
- Ban on ex post facto laws. This prevents Congress from making a particular action illegal retrospectively. That way, you can only be convicted of a crime if your act was illegal at the time you did it.
All of these are meant to prevent the government from abusing the rights of the people.