The former Love Island presenter took her own life last Saturday at the age of 40.
After taking light-hearted aim at the celebrities in attendance, Whitehall paid tribute to the presenter, calling her "one of the Brits family."
"She was a kind and vibrant person with an infectious sense of fun," he said. "She will be sorely missed.
"I think I speak for everyone here when I say our thoughts are with her friends and family."
Whitehall earlier took aim at Prime Minister Boris Johnson and Coldplay front man Chris Martin.
Listing the night’s performers and nominees, he described American singer Billie Eilish as the “only teenager who makes Greta Thunberg look lazy”.
Tributes have continued to flow for the late presenter, with Russell Brand and Laura Whitmore among those who have paid tribute to the star.
Harry Styles arrived on the Brits red carpet wearing a black ribbon, which fans have speculated is in honour of Flack. The pair briefly dated in 2011.
The Brit Awards are the first major public event since Flack passed away.
Follow live updates and highlights from the ceremony here.