On Wednesday, Kelly was asked again whether he planned to stay with the Niners. He repeatedly nodded in the affirmative before providing a response.
"Yep," Kelly said. "So we're all done with that, I hope."
Asked if there's any chance he will return to Oregon, Kelly shook his head and said "no."
Kelly said he called Helfrich, his close friend, on Wednesday morning to offer support.
"I have not talked to anybody at Oregon except for Mark Helfrich," Kelly said.
Oregon announced Tuesday night that it was parting ways with Helfrich after four seasons at the helm. He served previously as Kelly's offensive coordinator before being promoted to head coach when Kelly departed for the Philadelphia Eagles.
"I just felt bad for Mark," Kelly said. "I love him like a brother. He's a tremendous person. He's a hell of a football coach but he's an even better person. I just felt for him and the rest of the guys on that staff.
"It's an unfortunate thing that goes on in this profession. We all know about it when we sign up for [this], but when it happens you're still kind of taken aback by it."
As the coach of an NFL team in the midst of a 10-game losing streak -- and who enjoyed his greatest coaching success in Eugene -- Kelly has been connected by many to the Oregon job for the past couple of months.
Kelly welcomed Phil Knight, Nike's co-founder and the most prominent Oregon booster, as a guest to a game earlier this season, which further fueled speculation.
Despite Kelly's multiple declarations that he's intent on seeing through a turnaround in the Bay Area, the rumor mill continued to churn. Kelly was 46-7 in four seasons at Oregon, winning three Pac-12 Conference championships along the way.
Although Kelly said nobody at Oregon had reached out to him, he did express a willingness to help them in their search for a new coach if asked.
"I love everybody associated with the university," Kelly said. "They were fantastic. If I can help them, I can help them. My thoughts are with Helf right now."
Kelly's Niners played in Miami last weekend and are training at Central Florida this week before traveling to Chicago to face the Bears on Sunday. One reason the 49ers are here is because of Kelly's relationship with Central Florida coach Scott Frost, who served as offensive coordinator at Oregon and worked with Kelly there as receivers coach.
Frost is considered a candidate for the now-vacant Oregon job, sources told ESPN's Brett McMurphy. In addition, Oregon has reached out to representatives of Ohio State defensive coordinator Greg Schiano and South Florida's Willie Taggart, sources said. Western Michigan's P.J. Fleck also is expected to be contacted as well, a source said.