Onlookers observed three minutes of silence before listening to a cello composition by the Catalan musician, Pau Casals, called "The singing of birds."
No speeches were given at the sombre event.
Some of the thousands of messages people left at the train station in the days following the tragedy had been inscribed inside the monument, which was created by a group of young Spanish architects called Fascinante Aroma A Manzana (FAM).
Visitors to the site will be able to enter the dome, which aims to be an "immaterial space of light and silence" according to one of the FAM architects, Mario Gil-Fournier.
Sunday's commemoration came nearly a month after the beginning of a trial of 29 people charged with involvement in the attacks, which killed 191 people and injured 1,824.
The trial is due to conclude in June or July, and the seven main defendants face record total sentences of 270,600 years in jail.
Spanish law, however, prohibits anyone from serving more than 40 years behind bars.
The ceremony also came at a time when the issue of terrorism was proving a divisive force in Spanish politics.
On Saturday, the conservative Popular Party (PP), removed from power in elections three days after the blasts, organised a second mass rally in as many days against the government in Madrid for what they perceive as soft policy toward Basque separatism.
Hardliners within the PP and some sections of the right-wing media have continued to promote a "conspiracy theory" alleging the Basque separatist movement ETA might have colluded with Islamists in the attacks on crowded commuter trains and stations.