The suit, filed by the American Civil Liberties Union in 2005 on behalf of Daniel and Kathy Sheehan, maintains that the searches are an invasion of privacy.
The trial court and Court of Appeals had previously dismissed the suit before trial, on the grounds that the Sheehans had consented to the pat-downs by renewing their season tickets. Monday's ruling overturns the earlier decisions.
The ruling states that the Supreme Court overturned the Appeals Court's finding and remanded the case to the lower court for further review and fact finding.
The 49ers were disappointed with the court's interim decision but were gratified that it stressed that the lower court must consider the important role the 49ers have in protecting fan safety, said Lisa Lang, 49ers vice president of communications.
Lang said the pat-down searches, an NFL policy, were instituted in 2005 for security reasons.
"Nothing in the Supreme Court's opinion indicates that it thinks the pat-downs in fact violate the California Constitution ... and we're pleased with that," she said.
The lower court will be required to look again at the issue.
"So at this point," Lang said, "for the fans nothing will change. We'll continue the limited pat-down process and we'll continue to watch the lower court."
ACLU officials said the ruling shows that the Supreme Court agrees in principle that residents should not be subject to pat-down searches.
"Californians should not be forced to pay for goods and services with their privacy, whether it's admission to a football game, a shopping mall, or a college graduation," said ACLU-Northern California staff attorney Ann Brick.
ACLU attorney Margaret Crosby said the issues being reviewed in the case go beyond the 49ers stadium.
"The Court's decision protects Californians' privacy in their daily interactions with the businesses that are critical to our ability to participate in modern society, including banks, telephone companies and insurers," she explained.