The 27-year-old mistakes Jonze for fellow writer Alexis Petridis and claims he "was masked as a fan" and "was hiding sinister ambitions and angles".
"Maybe he's actually the boring one looking for something to write about," she said in a series of tweets, which have since been deleted.
Cue an onslaught of angry tweets from fans who stood by their seemingly morbid hero.
Jonze has responded to the pop star's criticisms by posting audio of his interview and writing this essay.
In it, Jonze writes: "Besides the fact Lana doesn't remember who actually interviewed her, there are a number of things about her statement that sound a bit iffy to me.
"She may well have not wanted to do the interview but it certainly didn't seem like it - she was delightful company for the 70 minutes we spent talking, and was happy to continue over the allotted time when the PR knocked on the door, an hour in, and asked how we were getting on.
"It's not pleasant asking a pop star if she thinks the idea of dying young herself is attractive - it's a dark question, but it's not a leading one. She has every opportunity to say no. And she can hardly complain about the subject matter: she'd been talking about her icons all dying young, she named her debut album Born to Die and had spent much of the 50 minutes previous to this point telling me how miserable she was.
"Ultimately, the problem with Lana's complaint is that she doesn't seem to know what she's actually complaining about," he wrote.
Del Rey said that she had disliked the media attention she had received - good and bad - since launching her breakthrough track Video Games in 2011.
"I never felt any of the enjoyment," she said. "It was all bad, all of it."
She also described how she longed to put an end to "everything".
But that's all in the past and now she "regrets ever trusting the Guardian".
Her disdain for life didn't stop her from reportedly singing at Kim Kardashian and Kanye West's wedding in May, nor from releasing her new album Ultraviolence, which went on sale last week.
Read more: TimeOut's four-and-a-half-star review of Lana Del Rey's Ultraviolence.
- Independent