The two paired up for the films Match Point, Scoop and Vicky Cristina Barcelona, but decided to take a break from collaborating so as not to burn out their partnership.
The Oscar-winning director said he is confident Johansson will appear in one of his films again soon.
Allen told Vanity Fair: "I have every intention of working with her again, but I just didn't think it was a great idea for either one of us to work together too intensely, picture after picture.
"I didn't want her to be burdened by, 'Oh, she's in all the Woody Allen pictures, it's so predictable', and she's my new muse, and all that silliness."
Johansson added that she's hopeful Allen will someday create a career-defining role for her.
"I don't think anything's played out. I'm waiting for him to write my Citizen Kane," Johansson said.
Allen recently changed the title of his Rome-set film from The Bop Decameron to Nero Fiddled.
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Watch the Match Point trailer below: