The 48-year-old actor - who is battling stage 3 colorectal cancer - had made his apologies for missing the spectacle, due to suffering from "two stomach viruses", but he shocked fans at the Richard Rodgers Theatre in New York City on Monday when he made a virtual appearance at the charity event.
In a prerecorded video, which was projected onto the stage, he said: "I have been looking forward to this night for months and months ever since my angel Michelle Williams said she was putting it together.
"I can't believe I'm not there. I can't believe I don't get to see my cast mates, my beautiful cast in person.
"And just I want to stand on that stage and thank every single person in the theatre for being here tonight. From the cast to the crew to everybody who's doing anything and has been so generous, and especially every single last one of you - you are the best fans in the world.
"Thank you for coming. It's just absolutely humbling just how much you did for this night, and I just want to say thank you. Thank you to every single person here."
As well as thanking the show's fans, he also introduced Lin-Manuel Miranda as his "understudy", and joked the Hamilton playwright was an "upgrade" on him.
He added: "And, obviously, on Dawson's Creek, I had an understudy, but this is a problem... and, we figured trying to find somebody who had never understudied in this theatre before."
Van Der Beek's appearance comes after he pulled out of the event, in which the cast of the hit teen TV show reunited for a live reading of the pilot episode in aid of the F Cancer charity.
Explaining his decision, the star - who portrayed Dawson Leery in the show - wrote on Instagram: "This is the evening I'd been looking forward to MOST since my angel Michelle Williams said she was putting it together, way back in January ...
"So you can imagine how gutted I was when two stomach viruses conspired to knock me out of commission and keep me grounded at the worst possible moment."
The event still went ahead with cast members Michelle Williams, Katie Holmes and Joshua Jackson.
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