"Tom is deeply saddened and is concentrating on his three children," his spokesperson said on Friday, adding nothing since despite mounting speculation about what led to Holmes's decision.
Their fairytale love affair had started so well. Cruise famously jumped up and down on Oprah Winfrey's couch professing his love for Holmes during a whirlwind courtship that culminated in a proposal under the Eiffel Tower.
But the divorce will be the third for Cruise, following his marriage to US actress Mimi Rogers from 1987-1990 and Australian Nicole Kidman from 1990-2001. He also had a three-year relationship with Spanish star Penelope Cruz.
Critics might suggest that, for all his blockbuster achievements on the big screen over the three decades, Cruise has been less successful in his personal life.
And he now faces a court battle royale for custody of the couple's six-year-old daughter Suri, after reports that Holmes is seeking sole custody because she fears Cruise wants to draw the child deeper into Scientology.
A lawyer for the Church of Scientology - of which Cruise is a prominent member - denied on Monday sending anyone to follow Holmes, or that Cruise wanted Suri to join the Sea Organisation, described as a boot camp for the religion.
"There is no truth whatsoever to the TMZ.com report (or any other report) that the Church of Scientology has sent anyone to follow or surveil Katie Holmes," lawyer Gary Soter told AFP in an emailed letter.
In the 26 years since he made his name in the first Top Gun movie in 1986, Cruise has established himself as one of the most powerful and bankable players in Hollywood.
That was confirmed again on Tuesday when the latest Forbes list of Hollywood's highest-paid actors put Cruise firmly at the top, with earnings of $75m between May 2011 and May 2012.
But TMZ reported that Holmes would get virtually nothing from a prenuptial agreement the couple signed - reports that she could get $15-20m are "absurd" - but that she does not mind.
"Money is not that important to her. She makes plenty on her own," it quoted a source close to Holmes as saying, adding that the only thing she will insist on is child support, which could turn into a "big ticket item."
A lawyer for Cruise, Bret Fields, said the Hollywood A-lister will file a rival divorce case, but for the moment is content to let Holmes's camp have the spotlight.
"We are letting 'the other side' (Katie and her team), play the media until they wear everyone out and then we'll have something to say," he told BBC radio.
"Tactically we can't say where Tom will file a divorce case and if he'll be seeking joint custody of Suri."
Amid all the bad news, Cruise had at least one supporter on Tuesday: Paramount came out swinging for him, as a trailer for his next movie Jack Reacher - due out in December - was launched in theatres.
"Tom is a huge movie star for the right reason, he's a very talented actor whose movies have entertained millions of fans," the studio said in a statement cited by The Hollywood Reporter.
"His ability to make a great movie, as we saw with the most recent instalment in the Mission: Impossible franchise - the most successful of the series to date - is the thing that moviegoers remember above all else."
Watch Tom Cruise's latest movie trailer for Jack Reacher:
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