The actor was DeGeneres’s guest for the third episode of the programme’s 18th season, which began on 21 September.
DeGeneres was asking Baldwin about his children when the actor decided to open instead with a few words of support.
“Before we talk about my kids, Ellen, I just want to say that you are someone – I’ve followed your career from when you were doing standup and you were a solo performer,” he told her.
“I’ve watched the films you’ve done and I’ve watched your success on this TV show, and you are one of the funniest and most talented women – one of the most funny and talented people in all of show business.
“We all have some patches of white water, but you keep going. Don’t you stop doing what you’re doing.”
DeGeneres acknowledged that there have been “some rapids” and assured Baldwin that she’s “maneuvering the raft”.
It was reported in July that The Ellen DeGeneres Show had become the subject of an internal investigation over allegations that it was a toxic workplace.
DeGeneres, who wasn’t personally a part of the probe, according to an NBC News source, has previously apologised in a note to staff, and spoke out about the situation in a lengthy monologue on the first episode of this new season.
“We have had a lot of conversations over the last few weeks about the show, our workplace and what we want for the future,” she told viewers. “We have made the necessary changes and today, we are starting a new chapter.”