Malik announced his departure from the boy band in March (15), and his work with the group prior to his announcement was recognised at the annual prizegiving as the Steal My Girl hitmakers picked up the Top Duo/Group trophy.
Liam Payne took the microphone after Niall Horan's acceptance speech to make sure his ex-bandmate was acknowledged.
He said, "This one is of course for the fans, but there's one more person to share this with and that's our brother Zayn."
One Direction also won a second prize for Top Touring Artist.
Prior to the heading into the event, Payne also noted Malik's departure, since it was their first awards show as a four-piece.
During an E! Live chat on the red carpet, he said, "It's obviously a difficult thing to talk about, but everything is all fine. We're all good with him and he's all good with us. He left for his own reasons and he's doing his thing now. You gotta do what you gotta do, but one of the awards tonight is also for him, so he's sharing the experience with us even though he's not here."
The nod appeared to end a Twitter feud between Malik and Louis Tomlinson, who took aim at his departed bandmate on social media after he announced plans to work on a solo project with DJ/producer Naughty Boy.
Tomlinson addressed the rift between himself and Malik following the war of words, which promped the ex-One Direction star to tweet, "@Louis_Tomlinson remember when you had a life and stopped making b**chy comments about mine?"
During an appearance on Thursday's (14May15) The Late Late Show in America, Tomlinson said, "There's been a bit of back and forth. I think we're on good terms again... I've never been very good at biting my tongue... Twitter's great for connecting with the fans but also if you feel like saying something you probably shouldn't, it's also good for that as well... It's all resolved."