The magazine, which had angered Muslims by publishing cartoons of the prophet Mohammed, was adopted after the attack as a symbol of free speech and the slogan "Je suis Charlie," or "I am Charlie," spread round the world.
The fifth anniversary has taken on fresh relevance this year because the first trial of people accused of involvement in the attacks is to begin later this year.
In Tuesday's ceremony, staff who survived the attack stood in the street outside as a bugler played the last post.
Among them was Laurent Sourisseau, a caricaturist who suffered a gunshot wound to the shoulder. He has since become the magazine's publishing director.
Also at the ceremony were the mayor of Paris Anne Hidalgo, Interior Minister Christophe Castaner, and Francois Hollande, French president at the time.
On Jan. 7, 2015, brothers Cherif and Said Kouachi had burst into the magazine's offices and opened fire with automatic weapons, killing 12 people and wounding several others.
They then ran out into the street and, a few meters (yards) away were challenged by a police officer, Lieutenant Ahmet Merabet. He was shot dead.
On Jan. 8 an accomplice of the brothers, Amedy Coulibaly, shot dead a female police officer in the Paris suburb of Montrouge and a day later, stormed a kosher supermarket east of Paris and killed four customers.
Wreath-laying ceremonies were held on Tuesday at the spot where Merabet was killed, and outside the kosher supermarket.
All three attackers were killed by police in different standoffs on Jan. 9. The magazine has since moved to new premises.The trial is due to begin later this year of 14 people alleged by prosecutors to have been accessories to the attack. They have been charged with financing terrorism, membership of a terrorist organization, and supplying weapons.