The bodies of Barbara Green and her daughter, Kristen Wormsley, 17, will arrive in the United States on Thursday, according to embassy spokesman Mark Wentworth.
He declined to give any other details.
Green worked in the U.S. Embassy administration section. Her husband, Milton Green, works in the computer section. He and the couple's son were injured in the attack.
Three other people were killed and 45 others were injured in the Sunday attack, when an assailant hurled grenades in the church, located in the guarded diplomatic quarter of the Pakistani capital.
The attack on the Protestant International Church prompted the State Department to warn Americans against traveling to Pakistan.
No group has claimed responsibility for the attack, but investigators focused on Islamic extremists who were outraged by Pakistani President Pervez Musharraf's support for the United States in its war on terrorism.