Benedict appointed the three men last year to investigate the origins of leaks, which revealed petty wrangling, corruption, cronyism and even allegations that senior Vatican officials conspired to out a prominent Catholic newspaper editor as gay.
The pope's butler was convicted of aggravated theft in October for having stolen the papers and given them to a journalist who then published them in a blockbuster book.
The three cardinals cannot share the full contents of their investigation, but it's unclear if they could give subtle hints about potential papal candidates to the electors. The Vatican's assertion that only the pope knew the contents of the dossier was a clear message to readers of Italian newspapers, which have run several articles purporting to know the contents of the report.
O'Brien's decision to remain home rather than participate in the conclave made his the first head to roll in the remarkable two weeks since Benedict, 85, stunned the world and announced he was becoming the first pope in 600 years to resign.
Monday's action marked a dramatic end to a career that got off to a rocky start when in 2003, as a condition of being made a cardinal, O'Brien was forced to issue a public pledge to defend church teaching on homosexuality, celibacy and contraception. He was pressured to make the pledge after he had called for a "full and open discussion" on such matters.
At the time, O'Brien said he had been misunderstood and wanted to clarify his position. But it's clear now he never really changed his mind. On Friday, three days before his resignation was made public, O'Brien told the BBC that celibacy should be reconsidered since it's not based on doctrine but rather church tradition and "is not of divine origin."
It appeared to be something of a parting shot, reasserting beliefs that he had kept quiet for a decade.
At home, at O'Brien's St. Mary's Roman Catholic Cathedral in Edinburgh, his decision was met with shock and disbelief.
"There are a lot of unanswered questions here, and I am unhappy about that. People can make such serious charges while remaining anonymous," said David Murphy, an administrator from Edinburgh. "It's like he's been hounded out of office without a proper chance to defend himself."
But Peter Mitchell, a churchgoer from Fife, conceded that the church may have to brace itself for scandal. "These don't appear to be random allegations. We are talking about three serving priests who are being very specific, and I don't think they would lie in this way."
O'Brien said in a statement that he was in "indifferent health" and had offered his resignation last November — a statement confirmed by the Vatican spokesman, the Rev. Federico Lombardi.
Lombardi said the pope had merely acted on the resignation now as he clears up final tasks before stepping down. Usually the pope waits until after a cardinal's 75th birthday to accept a resignation. In this case, Benedict acted a few weeks early.
Katz reported from London
Associated Press Writer Ben McConville in Edinburgh also contributed to this report.