York apologized to fans for the 2-14 season, and promised to help rebuild the 49ers culture.
"I am embarrassed. This is not acceptable to me," said York.
When asked if he should be dismissed, York responded in part: "I own this football team. You don't dismiss owners."
RELATED: Trent Baalke on being fired by Niners: 'It was the right thing to do'
York said he wished the firings of Baalke and Kelly had been cleaner.
"I didn't see the future going the right way and I didn't see us being able to reestablish that winning culture," said York.
Players say they found out about the changes in a text sent out last night, 49ers Center Daniel Kilgore says they plan to continue moving forward as a team. "There is no question from us. He's the boss. He told us what happened and we're rolling with it," Kilgore told ABC7 News.
Sacramento Bee 49ers reporter Matt Barrows tweeted that the team has interviews lined up this weekend with Patriots offensive coordinator Josh McDaniels, and Chris Ballard who's in the Chiefs front office.
As for the firings, Baalke says he found out on Friday that he won't be returning. Kelly found out after yesterday's loss.
This year's 49ers team ranks dead last in franchise history, matching their worst record ever at 2-14. Kelly had to deal with some big injuries this season, he was asked before being fired, if he would be surprised if the team let him go.
ABC7 Sports' Larry Beil talks Jed York, 49ers dismal season
"I don't think anything surprises me. I live my life in vision not circumstances; I control what I can control. What we control is how we coach our players and what we do with them, if that's good enough that's good enough. If it's not good enough, so be it," said Kelly.
Baalke is being blamed for depleting the team's roster, mainly because of poor drafting. A lot of fans feel, Baalke's firing was a long-time coming.
The coaching position with the niners has been like a revolving door. The team has had three different coaches over the last three years. Jim Harbaugh was at the help for four years but left the team in 2014 after failing to reach the playoffs that year.
Harbaugh was replaces for a single season with Jim Tomsula, who only got the 49ers five wins that season. The Niners then hired Chip Kelly, after he was fired a by the Philadelphia Eagles in 2015.
Click here to read more stories about the 49ers.