The Homeland Security Department oversees immigration applications, and will now allow legally married U.S. citizens to petition for a green card for their same-sex spouses the same way heterosexual married couples are allowed.
The court ruling and corresponding move was applauded by gay rights organizations on Wednesday.
"At long last, we can now tell our families that yes, they are eligible to apply for green cards," said Rachel Tiven, executive director of Immigration Equality, in a statement.
"Many of our families have waited years, and in some cases decades, for the green card they need to keep their families together. Couples forced into exile will be coming home soon. Americans separated from their spouses are now able to prepare for their reunion. Today's ruling is literally a life-changing one for those who have suffered under DOMA and our discriminatory immigration laws."
In a statement earlier Wednesday, President Obama said he was directing his Cabinet "to review all relevant federal statutes to ensure this decision, including its implications for Federal benefits and obligations, is implemented swiftly and smoothly."