The 'Killing In The Name' guitarist and his bandmates took to the stage as the opening act at the 1993 show with no clothes on, and he recalled how quickly the crowd turned.
He told Uncut magazine: "There was an outpouring of excitement among the crowd for the first five minutes. Then there was an interesting stand-off as it was clear this was not just some sort of quick stunt.
"Then then for the last five minutes there was outright hostility - booing and giving us the finger and quarter coins being thrown at our d****.
"The time I wish I had my pants on was when the police arrived.
Tom revealed he hid with members of Fishbone, because he knew he'd be able to fit in.
He added: "I ran to the only place that a naked black man might be undercover backstage at Lollapalooza, and that was the Fishbone tour bus...
"They were sitting around in various states of undress watching 'Star Wars', so I fit right in.
"Hopefully in some way we made the point that controversial music is not something you can take for granted, you have to fight for it. Although people just remember us standing there naked."
Meanwhile, the guitarist also paid tribute to Woody Guthrie and revealed the folk icon has his favourite guitar slogan.
He explained: "My favourite is not on my guitar, it's on Woody Gruthie's. 'This Machine Kills Fascists' is such an awesome, poetic treatise.
"I love using the guitar a canvas for additional sloganeering but it all goes back to Woody emphasising that these are not just songs to sing and dance to, there's serious business at hand with three chords and the truth."