"This is a great victory, a dream come true," Pires said as the couple kissed and hugged.
"Now we're a family, that's the important thing," Pires said, adding they would continue to fight for equal rights for homosexuals, including adoption.
The ceremony came less than a month after Portugal's conservative president ratified a gay marriage law passed by Parliament in January. His approval made Portugal the sixth in Europe to let same-sex couples wed.
The center-left Socialist government said the law is part of its effort to modernize Portugal, where homosexuality was a crime until 1982. Three years ago the same government lifted Portugal's ban on abortion, despite church opposition.
Pires and Paixao, the lesbian couple, had campaigned for a change in the law since a registry office turned them away when they first tried to marry in 2006.
Officials argued the law stipulated that marriage was between people of different sexes. The women appealed to Portugal's Constitutional Court because the constitution forbids discrimination based on sexual orientation.
The court rejected their appeal, but left-of-center parties in Parliament supported the government bill which removed the reference to marriage being between different sexes.