The 30-year-old actress visited Los Angeles Superior Court to process the paperwork, citing 'irreconcilable differences' as the reason behind the split.
Johnny, 52, met Amber on the set of the 2011 film The Rum Diary, and they married twice in February 2015, holding the first wedding in Los Angeles, and then following it with an idyllic ceremony on Johnny's private Bahamas island shortly afterwards.
In an interview with Elle in June of the same year, Amber said of their nuptials, 'Nothing is a dramatic change. We've been together for a long time now, so it's been a fairly organic process. I have a fiercely independent spirit.'
However, she added of Johnny, 'I fall in love again and again.'
According to TMZ, the Pirates of the Caribbean actor has hired top divorce lawyer Laura Wasser to deal with the split, and is said to be arguing Amber's case for spousal support.
Johnny, who is currently doing a promotional tour for his new film Alice Through The Looking Glass, has also been pictured on the red carpet without his wedding ring.
The news of divorce comes at an already difficult time for the actor, whose mother passed away aged 81 after a long illness earlier this week. He had a very close relationship with his mother, and has spoken out previously about his respect for her difficult upbringing.
'My mother was raised in a shack, in the wilds of Appalachia, where the toilet was an outhouse', he told Rolling Stone in an interview in 2013. 'She used to say she did the same things that her mom did – and her mom certainly didn't know any better.'
'With my kids [Jack and Lily-Rose, from Johnny's previous marriage to Vanessa Paradis] they're told 75 times a day that they're loved. One thing I know is they feel loved and secure and happy and needed and necessary and a part of something.'
Representatives for the couple have not yet released a statement on the split.