The 49-year-old supermodel posed with the grime star on the cover of the publication in May 2018, a time when they were rumoured to be dating, and she's admitted they initially arranged to have the pictures taken "on [their] own" but they turned out so well, she contacted the magazine in order for other people to get the chance to see the images.
She said: "Well can I tell you a secret about that, which I hope Skeppy won't mind? Junior actually, I don't call him Skepta, I call him Junior.
"We basically did that shoot on our own, it wasn't for any publication, and once I saw the pictures I was like 'no, no, no we should come out.' And so then I started making some calls.
"It wasn't like I was going to wait months for it to come out - it's either got to come out in the next few or it ain't coming out at all. So first I had to send someone with the pictures and da-da-da."
Naomi admitted Dylan Jones, the magazine's editor, had other plans for the cover, but he took a gamble on the model's request "for the culture" and she was glad it paid off.
She added: "And then, you know, of course Dylan [Jones] did have other people lined up for that cover. Dylan Jones from GQ, he had other people lined up, and so I was basically telling him 'unline them'.
"And I was like, 'You need to put this [on the] cover!' And actually I've gotta give him the credit, he did do it and he did push it up and it came out in March and I think, you know, for me it was for the culture. It was for us, it was for all of us.
Naomi had "fun" at the photoshoot with Skepta.
Speaking on 'The Norte Show' on Capital XTRA, she said: "It was fun shooting it, and Junior just loves the camera. He's great. And the whole team, we shot that in one day in New York, like hours., because I remember he got off a plane straight from London and came to the shoot."
And the former 'Empire' actress even poked fun at her rumoured romance with the 37-year-old musician.
After DJ Manny Norte introduced AJ Tracey and Skepta's new single 'Kiss and Tell', Naomi quipped: "We do not kiss and tell!"
When Manny laughed,"But we kiss though right?", she then replied: "We love to love..."
Tune into Manny Norte on Capital XTRA, week days from 10am - 1pm and every Sunday from 7pm - 10pm.