The pop star upset many young fans and their parents when video footage of himself and bandmate Louis Tomlinson smoking pot and joking about cannabis culture during a car ride in Peru surfaced last week (ends30May14).
Neither Malik nor Tomlinson had addressed the video or the fall-out from it before the band took the stage on Friday, but the singer took a moment to thank fans, stating, "Thank you for everything you've done for us from The X factor until now. You're the best fans in the world."
The controversy may have kept a handful of fans from attending the big gig, but the band still played to a full house as 90,000 devotees packed into Wembley.
Liam Payne was awestruck by the sight of so many people and told the audience, "Hello Wembley. I genuinely can't believe I'm saying that. Right now is the most surreal moment of my life.
"It's the best day of my life and you've made all our dreams come true."
He previously confessed that he had dreamed he was performing at Wembley naked the night before the concert.
Bandmate Niall Horan added on stage, "This is absolutely incredible. We were put together as a band less than 100 yards away from this arena and now here we are stood in front of you. We can't thank you enough."
Harry Styles took to Twitter.com after the concert to express his thoughts, writing, "Wembley. Wow. Thank you for a night impossible to ever forget."