Baalke had confirmed to a local radio station Sunday morning that he had been fired Friday, while Kelly said after the 49ers' loss in their season finale that he expected to meet with CEO Jed York to have a conversation about his future with the team.
"I have informed Trent and Chip of my decision to pursue new leadership for our football team," York said in a statement a short time later. "These types of conversations are never easy, especially when they involve people you respect personally and professionally.
"Despite my feelings for Trent and Chip, I felt the decision to change our football leadership was absolutely necessary. The performance of this team has not lived up to my expectations or those of our fans, and that is truly disappointing. We all expected to see this team progress and develop as the season went on, but unfortunately that did not happen. That is why now is the time to find a new direction for this team."
Kelly said before the team's announcement that he would not be taken aback if he were let go after just one season on the job.
"I don't think anything surprises me," Kelly said. "I live my life in vision, not circumstances, so I control what I can control, and what we can control is how we coach our players and the way we deal with them. If that's good enough, then that's good enough, if it's not good enough, then so be it. I'm proud of the way our guys played today."
ESPN's Adam Schefter reported Saturday night that the Niners would be dismissing Baalke and Kelly after Sunday's game.
Soon after that report came out, Kelly said, he received a call and a voicemail from York, and when he returned the call, he and York had what Kelly described as a "normal" conversation.
"It wasn't," Kelly said. "I love these players, so I think if I was distracted by anything else, I wouldn't be giving them what they deserve, and they give me everything on every day, so I have to give that back to them. Those guys are awesome.
"We have a bunch of guys who just competed and gave everything they had. One thing we talk about here all the time is don't complain. We're all privileged to play this game and coach this game, so every time you have an opportunity to do it, go out and do it."
Kelly said he didn't have any players asking him about his status before the game but acknowledged there were "a lot of hugs" in the locker room after it was over.
Kelly also said he didn't feel nervous about the meeting and that he didn't anticipate trying to plead a case to stay.
"I don't think I'm going to 'The People's Court,'" Kelly said. "He wants to have a conversation, so I'll have a conversation with him.
"I just think it's an end-of-the-year meeting, and we'll go discuss everything positive and negative about what went on this season and see what happened."
In the locker room, multiple players spoke out on Kelly's behalf while also noting that they understand the business side of the operation and the need for the 49ers to improve.
"He's a good dude," receiver Torrey Smith said. "I understand the business side of it. I think he's a good coach. I think he's a better person. But that's how this business goes. They let good people [go] in tough spots. When we lose like we did and have a season like we had, changes are made or can be made. From coaches to players, it's all of us and we were all a part of the problem. That's why our record was what it was."
Earlier, Baalke told the radio station that his firing "was the right thing to do."
"You know, I've been here since 2005, and I have a lot of respect for the organization as a whole, and the ownership, the fan base. It's difficult, but it's the right thing to do," Baalke told KNBR Radio.
Asked whether the organization needed sweeping changes, Baalke told KNBR: "Sometimes you need to reset the culture. When you have a winning culture, which we did in 2011, '12, '13 and '14, a lot of good football players. A lot of memorable games we went through together.
"Then you transition. At some point, those veteran guys move on. Blending in with younger guys, and sometimes it takes a little longer than you'd like. And this is probably one of those situations."
Baalke said the firing did not surprise him.
"We've done some awful good things," he said. "Some very successful seasons. Unfortunately regret we weren't able to bring a championship to the Bay Area, which they so deserve. I think The Faithful has been great. Wish this organization nothing but the best moving forward. I do see a bright future for them."