Niners CEO Jed York told Jim Kozimor on Yahoo! SportsTalk Live that he and Harbaugh mutually agreed to table talks toward a new deal until after the 2014 season.
"We actually just had this conversation yesterday," York said Thursday, via CSNBayArea.com. "Lots of people were talking to him about it. We just said, 'You know what, let's not do anything during the season. Let's sit down a week or so after the season is over and let everybody know we're not focused on anything that's off the field right now.'
"Jim and I will sit down a week or so after the season is over and we'll figure out where we go."
The decision could lead to a supreme windfall for Harbaugh if he's able to land a Lombardi Trophy this season. The Niners enter 2014 as one of the NFL's favorites to reach the Super Bowl.
"Well, Jim's here for the next two years under contract," York said. "And like I've said publicly and very loudly in the past, I hope he has the utmost leverage when we sit down and talk about his contract at the end of the season.
"It's a good thing. It's an unbelievable problem to have."
Tensions seems to have simmered between coach and team in recent months. Earlier this week, Harbaugh sounded like a man at peace with the process when asked about his future.
"I signed my 10th contract in the National Football League in 2011, so I understand contracts," said Harbaugh, who signed a five-year, $25 million deal in 2011. "I understand how contracts work, and what they are there for.
"I also know that I work at the pleasure of the San Francisco 49ers organization and at the pleasure of the York family. And I am paid extremely well -- which I am most grateful for, and I am very proud to be part of this organization."
Harbaugh has restored a winning tradition in San Francisco. He remains in the driver's seat in negotiations -- whether the Niners get over the Super Bowl hump or not.