Pete Doherty's band will join Avril Lavigne, Foo Fighters, Mika, My Chemical Romance, Nicole Scherzinger, Tokio Hotel and will.i.am at the event on November 1.
Model Lily Cole, Napoleon Dynamite star Jon Heder and singer Kelly Rowland will hand out awards at the show, alongside Boris Becker, Craig David, Dave Gahan, Good Charlotte, Joss Stone and Michael Stipe.
A statement on behalf of the band said: "Babyshambles are very excited to be playing the EMAs and looking forward to their trip to Munich."
The ceremony will be hosted by Snoop Dogg, with Wyclef Jean fronting a special backstage show for MTV.
It will also see the results of the first New Sounds of Europe Award, which celebrates emerging international artists.
Acts from Estonia, Romania and Turkey have triumphed as the finalists after almost two months of voting by MTV audiences across Europe. Viewers will vote online and by live SMS during the show to decide who is given the chance to perform onstage and win the award.