But the pair, who attended the star-studded ceremony at London's Royal Opera House, lost out to Kieran Evans, who wrote and directed the romantic drama Kelly + Victor.
However, Hooley said it was an amazing achievement for the two writers to secure a nomination.
And he said it could only help raise the profile of Northern Ireland as a significant hub for the film industry.
He said: “I couldn't be more proud of Glenn and Colin. Of course, it would have been lovely for them to win the Bafta. I would have been partying all night, but the champagne will have to wait.
“The fact they were nominated at all is a great honour for everyone involved in Good Vibrations, but particularly as it recognised the hard work and talent of Glenn and Colin.
“Their Bafta nod not only helps raise the profile of the film, but also shines a light on Northern Ireland as a great place to come to make movies. And hopefully it will encourage other young film-makers from here to give it a go.”
Hooley said he believed the low-budget indigenous movie would have a long shelf life.
“So many people who watched Good Vibrations have said that it will be a cult classic, a film that will still be around in years to come,” he said.
“And that's not a bad legacy.”
Elsewhere, Irish actor Michael Fassbender, whose mother hails from Larne, missed out on the Best Supporting Actor award.
The star of 12 Years A Slave, who grew up in Killarney, first came to prominence in the highly acclaimed Bobby Sands biopic Hunger, in which he played the republican hunger striker.
In 12 Years A Slave, directed by Steve McQueen, Fassbender plays the harrowing role of a slave owner. Best Supporting Actor was won by Barkhad Abdi for Captain Phillips.
There was good news for the movie Philomena, which was partly shot in Co Down.
Best actress nominee Dame Judi Dench spent four days filming in Killyleagh, Bryansford and Rostrevor, where she met some long-lost relatives.
The veteran star of stage and screen looked elegant in black velvet as she walked the red carpet.
Based on a true story of an Irish woman forced to give up her son, it scooped a Bafta for Adapted Screenplay for Steve Coogan and Jeff Pope. Accepting the award, Coogan praised the “real Philomena Lee”.
He said: “Her story has been told and her story finished in the Vatican. She has been heard but there are 60,000 women who are yet to trace their children”.
Film-maker Peter Greenaway, whose career includes art-house hits such as The Cook, The Thief, His Wife and Her Lover, was presented with the outstanding contribution award by Juliet Stevenson who said “he has no time for convention or orthodoxy”.
Among the stars who also shone last night was Gillian Anderson, star of Northern Irish crime thriller The Fall, who stood out in a vintage 1949 strapless colour-block blue dress.
The event, formally known as the EE British Academy Film Awards, was hosted by Stephen Fry. Welcoming the audience, Fry paid tribute to Dame Helen Mirren, joking that the actress — who has played the Queen on stage and screen — has “this year brought her grandson along. Welcome his Royal Highness the Duke of Cambridge”.
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