The band, who have been topping the charts for over 20 years, were named Best Irish Band - fending off serious competition from a wealth of talented newcomers.
U2’s latest effort, How to Dismantle an Atomic Bomb, meanwhile, scooped Best Irish Album.
Before a packed out Point Theatre, U2, represented by Adam Clayton, were also awarded the Best Live Performance for their three sell-out Croke Park gigs, which left music lovers scrabbling for tickets, last June, despite the surprise addition of an extra date, which sold out in just 90 minutes.
The musical talent was not the only attraction at the glitzy event as international stars of stage and screen were on hand to present awards including Golden Globe winner Jonathan Rhys Meyers, Kerry Katona, Stephen Rea, Gavin Friday, Liam Cunningham, Keith Duffy, Westlife manager Louis Walsh and former Boyzone member Stephen Gately.
Before presenting an award, Cork-born Rhys Meyers said it was not until he came home to Ireland that he realised the significance of scooping the Golden Globe for his portrayal of the King of Rock ‘n’ Roll in the mini-series Elvis.
The 28-year-old, who was accompanied by his girlfriend, said: “I was working the morning after, shooting a film. It wasn’t until I came home that I really knew what it was all about.”
The actor said he was looking to buy a house in Dublin as he will be filming in Ireland during the summer for a e20 million US Showtime drama series.
The actor will be playing another young King in that production.
“I’m going to be playing a young Henry VIII,” he said, “It’ll be fun.”
Another presenter, Keith Duffy, joked on a possible reunion of Boyzone: “You never know if Take That can do it.”
Duffy added that he did not miss Coronation Street and was looking forward to flying to Los Angeles where he had some auditions lined up.
Other guests included Divine Comedy singer Neil Hannon and lap dance impresario Peter Stringfellow and Joe Elliot.
Thousands watched performances from top Irish and international acts including Sugababes, McFly, The Darkness, Westlife, Jamie Cullum, The Pogues, Bell X1, Republic of Loose, Damien Dempsey and Gemma Hayes.
There were 17 awards handed out at the event, hosted by comedian Patrick Kielty, five of which were chosen by the public.
The Pogues received the Lifetime Achievement award.
The band, who were formed in 1982 by McGowan who is famous for his rotten teeth and hard drinking, went on to close the show with special guests The Dubliners with a rendition of The Irish Rover.
On his way into the event, McGowan strolled up the red carpet shouting “Irish Constitution”, before posing with The Pogues for some pictures.
“It is nice to be legend when you are still alive. A lifetime achievement award is not part of any job really,” he said.
Singer/songwriter Gemma Hayes was voted Best Irish Female by the public, while Damien Dempsey won his third Meteor Award for Best Irish Male.
Westlife won the award for Best Irish Pop Act for the sixth year in a row, whilst Today FM’s Ray D’Arcy made it two in a row for Best Irish DJ.
Dublin band Humanzi took Best New Act. 2FM listeners chose newcomer Laura Izabor as the Hope for 2006 Meteor Award.
Cork man John Spillane was presented with the award for Best Folk/Trad.
Britpop revivalists the Kaiser Chiefs won Best International Band and Best International Album.
The band members said: “We are very pleased - we like playing in Ireland, there is the best crowd. We are delighted to be here.”
On the Best International Album category, they joked: “Who else is there, there is no competition.”
US rap star Kanye West was named Best International Male and Gwen Stefani was named Best International Female.
Fr Peter McVerry, a campaigner for young homeless people, was presented with the €100,000 Humanitarian award.
The campaigner, who founded the Arrupe Society in 1983 to provide care and accommodation for homeless boys, was honoured for his tireless work.
Grammy Award-winning Riverdance composer Bill Whelan was given the prestigious Meteor Industry award for his work in the sector as a performer, producer and composer for 26-years.
The show will be broadcast on RTE2 at 9pm on Sunday.