The actress, 43, was introduced to the couple through a mutual friend and shared her experience of the occasion with US chat show host Andy Cohen on Watch What Happens Live.
While the Duke of Sussex "could not have been nicer", Wilson admitted that the Duchess of Sussex "was not as cool" with her.
She added that "Meghan wasn't as naturally warm" during the awkward encounter, which took place on an undisclosed date and possibly in California where they all live.
However, Wilson suggested that the duchess's reaction may have been as a result of her mother, Sue Bownds, asking the royal mother-of-two "slightly rude" questions.
She said: "My mum being Australian asked her all these slightly rude questions like, 'Where are your kids?' and things like that."
The star joked: "Maybe that's why she was like, 'Who are these annoying convicts from Australia?' I'm like, 'Mum, don't ask her that.'"
In November, Wilson announced the birth of her daughter Royce, born via surrogate with now-fiancee Ramona Agruma.
The couple, who revealed their relationship last summer, gave their baby girl the middle name Elizabeth "after the late Queen", Harry's grandmother.
Last month, exactly one year after Wilson hosted the Baftas, she revealed that she had asked Agruma to marry her with a diamond Tiffany ring.
The pair became engaged in a "magical surprise" at Disney, where they have since said they plan to wed at a later date.
Posting the happy news on Instagram, the Pitch Perfect and Bridesmaids star wrote: "We said YES!"
Watch: Rebel Wilson says Meghan Markle is 'not as cool' as Prince Harry