Twelve US states plus the District of Columbia now recognize same-sex marriage, but about 30 states have decreed that marriage can only exist between a man and a woman.
"Now we will be married and be equal to every other family in California," said Kris Perry, a plaintiff in the Proposition 8 case, alongside her partner Sandy Stier on the Supreme Court steps.
"Thank you to the Constitution ... but it's not enough," added Stier. "It's got to go nationwide. This can't wait decades" for marriage equality to be legalized in all 50 states.
Obama is the first serving US president to come out publicly in favor of marriage equality.
White House spokesman Jay Carney said the president had telephoned 84-year-old Edith Windsor, the plaintiff in the DOMA case, and "congratulated her on this victory, which was a long time in the making".
Obama also called Chad Griffin, head of the Human Rights Campaign, the leading US lesbian, gay, bisexual and transgender civil rights group, and the plaintiffs in the Prop 8 case to congratulate them on a "tremendous victory".
US social conservatives however were outraged.
"Today is a tragic day for marriage and our nation," said the US Conference of Catholic Bishops, which urged Americans to pray to God for a review of the Supreme Court's "wrong" decision.
Celebrations erupted across the US after the decisions were announced, including in San Francisco, home to largest gay community in the US.
AFP contributed to this story.