In his opening speech, President Putin declared that the CIS remained relevant more than 13 years after its creation.
He also stressed the key role it could play in fighting terrorism and extremism.
"It's precisely because of our efforts that the UN General Assembly proclaimed May 8th and 9th of this year as days of reconciliation and remembrance. And it has called on states to unite their efforts to combat the ideological successor of Nazism -- terrorism. And also ideological doctrines based on racism and xenophobia. I am convinced the CIS is capable of becoming an effective instrument for such a joint task," Putin said.
The summit was held on the eve of high-profile ceremonies to mark the 60th anniversary of the victory over Nazi Germany, which are due today to be attended by almost 60 heads of state.
The Russian-led gathering of 12 ex-Soviet states was founded in December 1991 in the wake of the Soviet Union's collapse. Of the 15 former Soviet countries, only the three Baltic States are not part of the CIS.
Yesterday's summit culminated in the signing of a "declaration of humanitarian cooperation" aimed at boosting cooperation between CIS members in the humanitarian, cultural, and scientific spheres.
The summit, however, was overshadowed by internal quarrels and questions about the CIS's viability.
Georgian President Mikheil Saakashvili announced last week his decision to boycott the victory-day celebrations and the CIS summit in Moscow to protest Russia's delay in withdrawing its troops from Georgia.
Azerbaijani President Ilham Aliyev also stayed clear of the CIS summit, saying he refused to meet with Armenian President Robert Kocharian as both countries continued to clash over the Nagorno-Karabakh enclave. Aliyev. however, is due to take part in today's celebrations in Moscow.
Recent uprisings that overthrew governments in Georgia, Ukraine, and Kyrgyzstan have highlighted Russia's fading influence on former Soviet territory. A few days before the summit, Russian Security Council Secretary and former Foreign Minister Igor Ivanov described the change of power in these three countries as unconstitutional.
The uprisings have also shown that former Soviet countries have increasingly opposed views on how their nations should develop.
While Ukrainian President Viktor Yushchenko and Georgia's Saakashvili are steering their countries westwards, Belarus and the four former Soviet Central Asian republics remain largely authoritarian.
The CIS has also so far failed to fully revive the former trade links between its members, a task that has topped the CIS's agenda ever since its creation.
More diplomatic spats erupted in the days preceding the CIS summit. Ukraine and Belarus exchanged angry words after five Ukrainians were jailed for taking part in a protest in Belarus.
Belarusian President Alyaksandr Lukashenka also slammed Saakashvili's decision not to attend the celebrations, saying he was too young to understand the contribution of Georgian veterans to World War II.
After the summit yesterday, participants were scheduled to meet war veterans from Russia and other CIS countries and attend a gala concert for veterans at the Bolshoi Theatre.