Wilken said the DOMA ban violated the U.S. Constitution's guarantee of equal treatment. She wrote that there was no proof the DOMA provision was "rationally related to a legitimate government interest."
Today's decision makes Wilken the second trial judge in the U.S. District Court for Northern California to strike down that section of the 1996 law.
U.S. District Judge Jeffrey White of San Francisco issued a similar ruling in February in a lawsuit filed by Karen Golinski, a federal appeals court staff attorney who wants to enroll her wife in the court's employee health plan.
An appeal of White's decision by a Republican-led Congressional group is slated to be heard by the 9th U.S. Circuit Court of Appeals in San Francisco in September.
The group, known as the Bipartisan Legal Advisory Group, is made up of the five top leaders of the House of Representatives. It stepped into both the cases before White and Wilken after the Obama Administration said last year it will no longer defend DOMA.
The group's three Republican members, including Speaker John Boehner of Ohio, supported intervening in the two lawsuits to defend DOMA. Its two Democratic members, including Minority Leader Nancy Pelosi of San Francisco, opposed doing so.
Another decision by a federal judge in Massachusetts striking down DOMA is on appeal before a U.S. appeals court in Boston.
In today's ruling, Wilken also struck down a U.S. Internal Revenue Service law to the extent that it bars domestic partners from enrolling in the long-term care insurance plan offered by CalPERS.
She ordered CalPERS to begin allowing gay and lesbian spouses and partners to enroll in the plan, but also said she will suspend that order during an appeal if the Congressional group files an appeal.
Wilken had indicated, in two previous rulings in which she declined to dismiss the case, that she was likely to strike down the DOMA provision.
The government-approved long-term care insurance plan offered by CalPERS gives participants federal tax benefits.