Bowlen, 70, had "taken a reduced role" in previous years, the team said in a statement to the paper, but now no longer officially has control of the team.
Team president Joe Ellis will take over control of the team.
"It's a really, really sad day," Ellis said. "It's sad for his family, his wife and his seven children. It's sad for everyone in the organization. And it's sad for all the Bronco fans who know what Pat Bowlen meant to them as an owner. It's a day nobody wanted to see happen."
Under Bowlen's ownership, the Broncos won a pair of Super Bowls with Mike Shanahan coaching and John Elway under center.
"The Broncos are very saddened that Mr. Bowlen is no longer able to be part of the team's daily operations due to his condition. We continue to offer our full support, compassion and respect to 'Mr. B,' who has faced Alzheimer's disease with such dignity and strength," the Broncos said in a statement. "As Mr. Bowlen focuses on his health, the Broncos have announced changes to their leadership structure that will ensure the long-term stability of the franchise."
Part of that structure will have Ellis serve as the team's steward moving forward, a plan NFL commissioner Roger Goodell acknowledged to the Post was fine, while also mourning the loss of Bowlen as an owner.
"This is a sad day for the NFL. Pat Bowlen's leadership has been critical to the success of the Broncos and the entire NFL," Goodell said. "From building a championship team that is a pillar of the community to his important work for the league on television and labor matters, Pat's love of the game drove him and we have all benefited from his passion and wisdom. But the time has come for Pat to focus on his health and we fully support him.
"Joe Ellis has been a trusted executive for Pat for many years after working with us at the league office. Joe's deep experience ensures that the Broncos will continue to have strong leadership."
According to the team's statement, The Pat Bowlen Trust was established in order to properly assist in a succession plan.
It's "overseen by non-family trustees" and focuses on the goal of keeping "the Broncos in the Bowlen family."
"Mr. Bowlen's long-term hope is for one of his children to run the Broncos at the appropriate time, and his succession plan will continue to be implemented by our organization in compliance with NFL ownership policies," the team said in a statement.
"Going forward, Pat Bowlen's indelible contributions to the Broncos, the NFL and this community will continue to define his three decades of ownership and serve as the standard he has set for his franchise."
Bowlen has more than 300 victories as owner including his two Super Bowl victories and six AFC Championship titles.
Back in June, CBS Sports NFL Insider Jason La Canfora had this to say on the long-term plans of the Broncos, which could involve some prominent names eventually taking over:
Many around the league believe executive John Elway, long like a son to Bowlen, could eventually be a part of a group that might take over the team, and while current Broncos quarterback Peyton Manning has been most closely linked to eventually joining Jimmy Haslam's ownership group in Cleveland, perhaps it's not out of the question two Hall of Fame quarterbacks unite as part of a conglomerate to take over the Broncos in time as well.