"We've got more work to do to ensure that government treats all its citizens equally, to fight injustice and intolerance in all its forms and to bring about that more perfect union," Obama said.
The signing followed sharp criticism of the president over a Justice Department motion filed last week in support of the Defense of Marriage Act - which effectively bars the federal government from recognizing same-sex unions.
Obama said he still wants to repeal the act.
"I believe it's discriminatory. I think it interferes with state's rights, and we will work with Congress to overturn it," he said.
The memorandum he signed Wednesday means same-sex partners of civil service employees can be added to the long-term care program, employees can use their sick leave to take care of domestic partners and children and same-sex partners of Foreign Service employees will be included in medical evacuations and housing allocations, according to the White House.
But it does not cover full health-care coverage, which would require an act of Congress, White House spokesman Robert Gibbs said.