Taking to the stage in an eye-catching blue fitted gown, Holly, 36, looked sensational as she presented the award for Virgin TV Must See Moments alongside the comic.
But when the popular host started presenting the awards and said the category was full of unforgettable moments, Alan, 40, made a cheeky jibe.
He said: “They should have waited until tomorrow when you will no doubt be p****d on This Morning again.”
Red-faced, Holly looked down as she joked: “Oh the shame!”
“I think being drunk on TV cheapens the art, if truth be told,” quipped Alan.
Alan referenced an episode of This Morning when Holly and her co-star Phillip Schofield appeared worse for wear in the same clothes as the night before, after they celebrated their win at the National Television Awards.
And viewers at home couldn’t wait to comment about the dig on social media.
One person wrote: “Alan Carr just went in on Holly.”
“Alan Carr & Holly Willoughby haha!! Perfect intro,” noted another fan.
One viewer noticed Alan swore before the 9:00pm watershed: “#BAFTATV crying because Alan Carr forgot it’s not past the watershed HAHAHAHA love him.”
Whilst another wanted Holly to turn up worse for wear again, they wrote: “You look lovely and if you don’t turn up to #thismorning tomorrow drunk – Ill be a disappointed viewer.”
Meanwhile, Emmerdale were honoured with the Best Soap gong for the first time in 16 years last night after fending off stiff competition from EastEnders, Casualty and Hollyoaks to win the coveted award.