But the new federal tax policy "certainly does not end the complexities that exist because we have a patchwork of marriage laws in this country," according to Brian Moulton, legal director of the LGBT rights organization Human Rights Campaign.
Same-sex couples living in a jurisdiction that does not recognize their marriage would still have to file any state taxes separately.
And the exclusion of domestic partnerships and civil unions from the change should signal to states that those arrangements, "while positive steps for protecting those families, are not equality," Moulton said. "We encourage states that can to finish that journey" to legalizing same-sex marriage.
Beneficiaries of a private Medicare plan will also be able to enter the same nursing home as their same-sex spouses, the Department of Health and Human Services announced.
The policy deals only with seniors whose same-sex spouse is receiving care in a nursing home under a private Medicare plan. Previously they may have faced the choice of receiving their own care in another facility away from their spouse or disenrolling from their plan to enter the same nursing home and paying more out of pocket, the agency said.
"Today's announcement is the first of many steps that we will be taking over the coming months to clarify the effects of the Supreme Court's decision and to ensure that gay and lesbian married couples are treated equally under the law," Health and Human Services Secretary Kathleen Sebelius said.
The Supreme Court's ruling on the Defense of Marriage Act has wide-reaching implications for federal benefits, but individual policies are being clarified by the agencies that administer them.
Last month, the Department of Homeland Security announced that U.S. citizens would be able to sponsor their foreign same-sex spouses for green cards. The Social Security Administration has begun offering partner benefits to same-sex couples, but only in those jurisdictions where their marriage is recognized.
Earlier this week, the Department of Veterans Affairs said that it might not be able to extend spousal support to same-sex couples because a portion of the U.S code governing veterans defines a spouse as person of the opposite sex.