"I want to congratulate all citizens of the Russian Federation—residents of the whole country, Crimea and Sevastopol—on what is, without any exaggeration, a banner event," Putin told a small group of senior lawmakers and officials before signing the documents.
They stood for the national anthem after the signing ceremony and Putin shook the legislators' hands.
Loyal lawmakers had rushed the legislation through both houses of parliament after Putin signed the treaty on Tuesday during a more elaborate Kremlin ceremony anchored by a fiercely patriotic speech.
(Read more: Crimea, Scotland…now Venice votes on breakaway)
Russia's annexation of Crimea, which has a narrow ethnic Russian majority and was given to Ukraine by Soviet leader Nikita Khrushchev 60 years ago, has touched off the biggest East-West crisis since the Cold War.
Crimeans voted overwhelmingly to join Russia in a referendum on Sunday that the United States and European Union say was illegitimate. They say Russia forces took control of the peninsula before the vote, and have imposed sanctions on senior Russian officials, lawmakers and allies of Putin.
(Read more: EU adds 12 names to Russia sanctions, mulls further steps)