The crowd at the ceremony reacted negatively to the mention of his name as his band Guns N' Roses were inducted, Reuters reports.
Rose had earlier in the week announced his refusal to attend the event, as he didn't feel "wanted or respected" by his former bandmates.
As Rose's former bandmates Slash, Duff McKagan, Steven Adler and Matt Sorum were on stage collecting the award, presenter Billie Joe Armstrong of Green Day asked the audience who was missing, prompting a reaction of boos.
Armstrong said to the audience: "Most singers are crazy, I can vouch for that. He is one of the best front men to ever touch a microphone. Sometimes you have to look back at chapters of your life to move forward."
Axl Rose became the first person to snub the awards event since the Sex Pistols failed to attend in 2006.
Rod Stewart also had to cancel his appearance with The Faces due to illness, with Simply Red's Mick Hucknall coming in to perform with the band in his absence.
The Beastie Boys were also forced to cancel their scheduled performance after Adam Yauch (MCA) fell ill.
The Red Hot Chili Peppers and Laura Nyro was also honoured at the awards ceremony.
Highlights of the 2012 Rock and Roll Hall of Fame induction gala air on May 5 on HBO.
Watch the video for Guns N' Roses' 'November Rain' below: