Flood and Alan Moulder have won UK producer of the year at the Music Producers Guild (MPG) Awards, automatically earning a Brit Award.
The duo produced Foals' album Holy Fire, which also beat James Blake and Laura Marling to win album of the year.
The band's Edwin Congreave said they played "a huge part" in making the album, and tracks such as My Number "wouldn't have happened" without them.
Trevor Horn was handed the evening's outstanding achievement award.
The producer, who has worked with Grace Jones, Seal and Frankie Goes To Hollywood, said he was "very flattered" to be honoured by people in the same business as him.
Seal was at the London ceremony to present him with his award, along with Radiohead producer Nigel Godrich. The singer paid tribute to Horn backstage.
"I don't think it would have been possible for me to have had the career that I've had and enjoyed the success that I continue to enjoy without Trevor Horn and [Horn's wife] Jill Sinclair being in my life," said Seal.
"He is a huge influence. He pretty much taught me what I know in terms of my trade in the music industry," added the singer.
He later joined Horn on stage to perform their Grammy Award-winning hit Kiss from a Rose, and whipped the crowd into a frenzy by taking the floor while singing Crazy.
Other winners included Disclosure brothers Guy and Howard Lawrence, who were handed breakthrough producer for their debut album Settle. The album is in the running for four Brit Awards at next week's ceremony.
Everything Everything's Kemosabe was named UK single of the year, collected by the band's Alex Robertshaw and Michael Spearman and their "very talented" producer David Kosten, who they have previously called their "fifth member".
"David was very generous saying we co-produced it, I'm not sure that that's true," said Spearman.
"But we do care about the sound and production of our records. It's kind of just as important as the song writing in a way, so [the award] means a lot."
The track beat Adele's Skyfall, from last year's UK producer of the year winner Paul Epworth, and Foals track My Number to take the prize.
Unreleased Bowie songs
David Bowie's innovation award, in recognition of his comeback album The Next Day, was collected by producer Tony Visconti.
"On behalf of my friend David Bowie it feels absolutely great," he said, admitting that he and Bowie had no idea if the album was going to be a hit or not.
"We were very excited with the reaction. Honestly I was in a daze for the first week, because keeping a secret for two years took quite a lot of lying. I almost started believing my own stories!" said Visconti.
"No one believed that David Bowie was going to make another album and so the timing was perfect, because everyone kind of gave up on him," he said.
"There were rumours of bad health and rumours of retirement, and I'm laughing my head off every time I hear them.
"I'm in the studio with a very healthy man who has no problem writing songs, he wrote easily 30 songs for that album," added Visconti, who hopes that two or three "astounding" leftover songs may still be released one day.
Foals producers Flood (Mark Ellis) and Alan Moulder beat competition from two previous winners, Paul Epworth and Ethan Johns to take UK producer of the year, which automatically wins them this year's best producer Brit Award.
"We're fussy about who we work with together," Moulder told the BBC, clutching the duo's glowing Philip Treacy-designed Brit award backstage.
"The great thing about picking a band like Foals is our sensibility is the same. You are only as good as the band you get to work with and their ideas and their ambition, where they came from, it was where we wanted to be - so it was a good choice."
The band, who are currently in the middle of a UK tour and play two dates at Alexandra Palace this weekend, said the producers "pulled it out of the bag" with the track My Number.
"Without them we wouldn't have been able to do it. It had a lightness and frivolity to it, but as soon as it went into the studio it had all these different layers," said Congreave.
"They made it into probably one of the best songs we've ever done, I think it's a perfectly produced pop song."
The MPG inspiration award was won by recent Daft Punk collaborator Nile Rodgers, while international producer of the year was awarded to Rick Rubin.
MJ Cole was named remixer of the year and Sean Davies, who was the first person to ever cut an acetate for the Rolling Stones, was handed a special recognition award by Bill Wyman.
Radiohead's Colin Greenwood presented the studio of the year award to Rak Studios, where the band recorded their album The Bends with producer John Leckie.
"We were a bunch of country boys from around Oxford, and that was our first city studio experience. Last time we'd been in the studio was Chipping Norton recording Creep.
"It was fantastic, the people there were great, that place is amazing," he added.
Radiohead also credit Rak Studios with being the place where they met future producer Nigel Godrich.
"And the rest is history," added Greenwood.