"When I look at our team and our performance on the field... and that's the bottom line, we just hadn't gotten it done," says York.
The question now, where does this once-proud franchise go now, after failing to make the playoffs for eight straight seasons?
For now all we know for sure is that defensive line coach Jim Tomsula will serve as interim head coach for this Sunday's season finale. On Monday at a news conference, York tried to clear up his team's future, but with the process just starting, there remain a lot more questions than answers.
After replacing Mike Nolan as interim head coach halfway through the 2008 season, team president York took the interim off Singletary's title. However, almost two years to the day Singletary was made the Niners 16th head coach, the Niners are looking for a new one, but first York wants to find a general manager.
"And I think if you look at some of the teams that have been successful out there, it's not about hiring the flashiest name as your GM or head coach or both, it's about making sure that the GM and the head coach are really working together," says York.
And who does the 29-year-old plan to get advice from?
"I think my uncle is probably the best person out there for me to talk to. There's a lot of other people that I will talk to, but my uncle is a person I'll get the most advice from," says York.
York has not set a timetable but understands the clock is ticking.
"We want to talk to a lot of people this week obviously. Obviously, there are a lot of people that are experienced, qualified, that aren't with teams and we're going to try to knock out as many people as we can this week," says York.
While some were surprised at the timing of the firing, York admits he thought about making a move several weeks ago.
"I think we had a chance to be a playoff team this year and I didn't think that making that change would have been the right decision for the team. Maybe in hindsight that was a wrong decision," says York.
Players themselves are in a state of shock.
"We're talking to each other, but we're really not trying to talk about the situation right now of coach Singletary. We're just not in the mood to talk about that right now," says 49ers defensive tackle Ricky Jean Francois.
Singletary released a statement on Sunday saying, "One of the greatest experiences of my life was having the opportunity to coach the 49ers. I'm thankful to the York family for giving me the opportunity to be a head coach in the NFL. I'm indebted to them for that. I'm also thankful for the Faithful fans. I'm just sorry I couldn't give them more."
With Singletary now gone, defensive line coach Jim Tomsula will serve as interim head coach this Sunday against the Arizona Cardinals. Monday, Tomsula met with the media.
"I want to reiterate my respect for Mike as an individual. I've learned at lot with Mike the last few years with him being with the San Francisco 49ers," says York.
Tomsula called Singletary a good man and says no one has to worry about his future.
As for the season finale, how was he approaching the contest?
"I break this whole thing down into a one-way calendar. That's what we have. When you get into the season, you get a one-way calendar. The long-term goals are Sunday. That's what make it a little bit unique. So what are we looking to do? We're looking to win a game, we're looking to prepare to win a game on Sunday," says Tomsula.
Like Singletary, Tomsula did not say who would start at quarterback. As for the players, they would love nothing more than to go out a winner.
"I'm very confident about the way things are moving. Going forward, we have a lot to look forward to," says tight end Vernon Davis.
"I was like saying we're going to win the NFC West and the one thing I can say, I apologize to Jerry Rice, Ronnie Lott, all the older guys who used to play here for coming out with a record like this and I feel like I'm disrespecting them because they're the guys who started the franchise and started to look like one of the biggest franchises in the league," says Francois.
In addition to firing the head coach, the 49ers have also let go of assistants Vance Singletary and Al Harris.
Two weeks ago, ABC7's Larry Beil caught up with former 49er great Steve Young. He asked the hall of fame quarterback what he thinks of the franchise as opposed to when he played.
"It's just about where we are as an organization. We got to get so we get stability. Six offensive coordinators in six years? That's the stuff that... you just can't do that. So, I refuse to get too tough on anybody with the instability," says Young.
The 49ers' recent struggles pre-date Singletary -- this franchise that won five super bowls from 1982 to 1995, has not had a winning season since 2002.
Here's how the team has fared since then: they have an overall record of 45 wins and 82 losses, the team's best season recently was last year, finishing 8-8 under Singletary, but the worst season came in 2004, with an NFL worst, 2-14.
This year, Singletary fired offensive coordinator Jimmy Raye after Week 3, then lost secondary coach and special assistant, Johnnie Lynn, when he resigned for personal reasons earlier this month.
Singletary switched quarterbacks three different times, starting with Alex Smith, going to Troy Smith for five games even after Alex Smith's hurt non-throwing shoulder had healed, then back to Alex Smith for two games before Troy Smith started Sunday -- only to give way to Alex Smith in the fourth quarter after Troy Smith had a heated exchange with Singletary.
"I'm not worried about individual things like that. What bothers me is we come in here, this is a playoff-caliber game, and we didn't get it done," says York. "And that's the bottom line."
The Associated Press contributed to this report.