The film is a semi-fictional retelling of the production of Wiseau's 2003 film "The Room", labelled as "the worst movie ever made."
The 39-year-old actor accepted the award alongside Wiseau, while noticeably blocking him away from taking the microphone onstage.
"'Golden Globes, so what? I'm not invited. I know they don't want me, guy with accent, long hair. So, I show them. I don't wait for Hollywood, I make my own movie,'" Franco said, quoting Wiseau.
"I'm very happy to share this moment with him today," he added.
"This was billed as a movie about making the best worst movie ever made," the four-time Golden Globe nominee said as he held his trophy, "but in fact it's a story about friendship."
Franco ended his speech thanking his longtime friends, including costar Seth Rogen, and his younger brother, Dave.
"I always said I wanted my own Coen brother, someone to collaborate with. I realise this year I had my own Franco brother. I love him more than anything," he said.
Many on social media felt for Wiseau and criticised Franco's mic block gesture.
Singer-actor Sara Bareilles called the moment "brutal".
"I'll never stop laughing at Franco shoving Wiseau away from the mic," another Twitter user wrote.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)