Helfrich's promotion does not come as a surprise. Before Kelly left for the NFL's Philadelphia Eagles on Wednesday, the Ducks' quarterbacks guru was considered the front-runner for the position.
Oregon confirmed the news first reported late Saturday night shortly before a scheduled news conference with athletic director Rob Mullens.
"We were looking for a coach who exemplified excellence, leadership and character, and who would embrace what our winning football culture is all about," Mullens said in a statement. "We found that person in Mark. He is a man devoted to his family, to his players and to this university and community. I am excited to see him lead the Ducks to even greater heights."
Sources who spoke on the condition of anonymity because the it had not been announced also said Oregon promoted wide receivers coach Scott Frost, the former Nebraska quarterback, to offensive coordinator.
Oregon, ranked No. 2 in the final AP Top 25, went 12-1 this season capped by a victory over Kansas State in the Fiesta Bowl.
Helfrich is from Oregon and was appointed offensive coordinator of the Ducks when Kelly took over four seasons ago. The Ducks have appeared in BCS bowls each of those four years, including an appearance in the national championship game against Auburn in 2011.
Before joining the Ducks, the 39-year old Helfrich was quarterbacks coach at Colorado from 2006-08.
Kelly came to the Ducks in 2007 as offensive coordinator under coach Mike Bellotti and is credited with creating Oregon's innovative hurry-up spread offense. Kelly went 46-7 at Oregon.
It had been widely expected that Kelly would jump to the NFL, leaving many surprised when he announced he was staying at Oregon after interviewing with Philadelphia, Cleveland and Buffalo following the Fiesta Bowl. Nine days later, however, he changed his mind and decided to go to the Eagles.
Just hours after Kelly's departure was announced, Oregon posted a job for a new head coach on its website. Under state law, Oregon was required to interview at least one qualified minority candidate for the job.
Oregon athletic director Rob Mullens said at the time that Oregon had already started the process of naming a replacement for Kelly following the Fiesta Bowl. He had set no timeline for replacing Kelly, except to say the Ducks would "move as fast as we can."
"We had already done a lot of groundwork, we had already started the process, knowing that Chip was going to be talking to the Eagles, Bills and Browns. We had geared up our process. We had obviously shut it down, but it's easy to click right back on."
At the time, Mullens also said there were internal candidates, but there was "no leader in the clubhouse."
Former Stanford offensive coordinator Pep Hamilton acknowledged Saturday that he interviewed with Oregon before he was hired by the Indianapolis Colts' to be their offensive coordinator.
Helfrich becomes the third straight offensive coordinator Oregon has promoted to head coach. Bellotti took over following Rich Brooks' departure.
Not much is expected to change under Helfrich, who is himself following Kelly's "Next Man In" philosophy.
As offensive coordinator, Helfrich has been in charge of Oregon's quarterbacks, guiding both Darron Thomas and redshirt freshman Marcus Mariota.
This season Mariota set the team's single-season record with 38 touchdowns (32 passing, 5 rushing, 1 receiving), surpassing the previous mark of 36 held by Thomas (2011) and Akili Smith (1998).
The first freshman named to the Pac-12's all-conference first team in 23 years, Mariota passed for 2,739 yards, completing a school-record 68.5 percent of his passes. He had 3,429 yards of total offense, second only to Smith's 3,947 in 1998.
Thomas, his predecessor, passed for 2,761 yards and a school-record 33 passing touchdowns his junior season last season despite missing a game because of an injury. He left school with a year of eligibility remaining in hopes of playing in the NFL but went undrafted.
Frost, 38, came to Oregon in 2009 after serving as an assistant at Northern Iowa. He played seven seasons in the NFL after leading the Huskers to the national title over Tennessee in the 1997 Orange Bowl.