The iconic superheroes begin a romance in this week's Justice League #12, a development which Lee claims could have "huge ramifications" for the DC Universe.
"This has been in the works for some time and we certainly wouldn't have pulled the trigger on it without there being great creative benefit to the liaison," he told The AP.
"Beyond the joy and sorrows of new love, there are potentially huge ramifications and dramatic ways this single relationship between these iconic characters will change the entire political and interpersonal landscape of the DC Universe."
Earlier this week, DC teamed up with online dating website Match.com to promote the romance by adding official Superman and Wonder Woman profiles to the website.
Justice League #12 was released in stores today (August 29).