The Big Bang Theory star cited "irreconcilable differences" in the legal papers, according to reports, and listed the couple's separation date as 3 September.
Kaley's papers, filed at Los Angeles Superior Court, also reveal the couple signed a pre-nuptial agreement ahead of their wedding, but provides no details as to the content of that document.
They married on New Year's Eve 2013 after a whirlwind romance: Kaley revealed they'd moved in together the day after being set up on a blind date, an engagement came after three months, and the marriage after six.
In a statement announcing their split over the weekend, actress Kaley's rep said: "Kaley Cuoco and Ryan Sweeting have mutually decided to end their marriage. They ask for privacy at this time. No further statement will be issued regarding this matter."
Fans were surprised by the news as in April this year Kaley had fiercely denied trouble in their relationship.
She had said: "I have never been more proud of anyone on this planet. This guy is fighting back from a whirlwind of injuries and not to mention constant 'conversation' regarding our marriage and basically any daily decision we decide to make."
"All of you who take it upon yourselves to trash our marriage, daily workings of our relationship and everything in between, go ahead and keep doing it, cause it only makes us stronger - if you were smart, you would take a look at your own marriage, relationship, job etc, instead of focusing on someone else's.
"You might be surprised at what you find. 'You know my name, not my story'."