In its place, Turner plans to launch a new title, Ben 10, which will feature one of Cartoon Network's highest-rating shows.
Alan Fenwick, vice-president of Cartoon Network Enterprises, said that the revamped magazine is expected to launch later this year.
He added: "Like much of the media landscape, publishing is changing. We felt the Cartoon Network magazine had to evolve to reflect this. It had increasingly become a showcase for our hit show Ben 10, and, recognising the brand's popularity, we took the decision to launch a Ben 10 magazine in its place, which will also include a Cartoon Network section."
Panini marketing director Mark Warsop said sales had declined as a result of "extremely tough competition" in the market and a lack of strong new children's characters for the brand. Sales are believed to have fallen to around 25,000 copies a month, from an ABC peak of more than 58,800 in 2002.
Panini, which also publishes magazines including Looney Tunes, Scooby Doo and Tom & Jerry, has an estimated 8.4% market share of the children's publishing market, placing it behind market leaders BBC Worldwide and Egmont.
Elsewhere within the children's market, Egmont Magazines has closed its Winnie the Pooh, Lazer and Daisy titles as it moves to invest in new brands. The publisher plans to launch two magazines for licensed children's brands in the spring.