My feeling would be that it is analogous to the individual party autonomy and a private law contract: You are free (within statutory limits) to contract whatever you want (or rather: can agree on). Once you have concluded the contract you must follow the rules set out therein. Thereby the contract could be said to limit your autonomy.
For a state that would mean that as soon as the state becomes a party to a treaty, it has to adhere thereto. That might be seen as limiting the sovereignty, but that limit was willingly accepted by signing the treaty.
I would just like to point out that pacta sunt servanda is not only a maxim, but also a norm expressed in Article 26 of Vienna Convention on the law of Treaties where there is a reference to the so-called "good faith".