It was met with silence from the stunned hosts, and tears from the show's producer Sam Baxter, who could be heard crying on air.
"Oh my goodness, are you kidding me?" Barnett said. "That's so uncool."
"That is truly disappointing. People think that's actually funny, that's not funny. That is probably one of the more disappointing, shameful things.
"Let's apologise on behalf of The Edge for their poor taste. I hope The Edge is going to make an apology as well."
Fellow host Gary McCormick added: "Pretty low rent, guys."
MediaWorks has been contacted for comment about whether there will be disciplinary action.
Barnett had campaigned for two weeks to interview Cruise, and said he was so nervous about finally meeting his childhood hero he couldn't sleep last night.
He said the show was inundated with text messages of support, and Facebook and Twitter users have since expressed their disappointment about the fake interview.
The last seven tweets on Si & Gary's Twitter page were promoting the interview.