The host poked fun at Fassbender's full-frontal nudity in Shame in his opening monologue, saying that he was afraid to "arouse" the actor.
"He's sitting in the second row... I could lose an eye," Brand said.
He went on to reveal that he went to school with the 35-year-old actor.
Later in the monologue, Brand revealed that the last time he hosted an MTV awards show, he met his wife Katy Perry. He said he hopes to meet his next spouse tonight (June 3).
"Fassbender!!! It has to be," he declared, pointed to the actor.
Brand also teased stars including Justin Bieber and Kim Kardashian during his opening speech.
The 2012 MTV Movie Awards continue to air live from the Gibson Amphitheatre in Universal City, California through 11pm on MTV. The awards will air on Monday, June 4 at 9pm in the UK.
> MTV Movie Awards 2012: Live blog
> MTV Movie Awards: Russell Brand wants to 'marry' Michael Fassbender
> MTV Movie Awards 2012: The winners in full
Watch Michael Fassbender talking to Digital Spy about his new movie Prometheus: