The evidence collected in the 1997 Woodlawn case matched evidence from a 1993 city case, where police identified Ronald White, 49, as a suspect, police said.
Wicomico County case found collections of DNA samples unconstitutional and that the practice provided access to a significant amount of personal information.
The U.S. Supreme Court will review the Maryland law next year. The court's decision will determine whether the practice can continue in about half the states that have authorized its use.
White, of the 2800 block of Forest Glen Road, was arrested Oct. 11 and indicted Nov. 5 in the 1997 case.
The victim told officers she found a man in her living room in her apartment in the in the 1600 block of Bluffdale Road. She ran to her bedroom and locked the door, but the man kicked open her door and threatened her if she screamed or looked at him. She believed he had a weapon.
After she was sexually assaulted, her attacker left the room, and she jumped from a second floor window and ran to a neighbor's apartment for help, police said.
White remains in custody at the Baltimore County Detention Center.
Baltimore Sun reporter Yvonne Wenger contributed to this article.