American businessman Kroenke currently owns 67 per cent of the Gunners through his company Kroenke Sports and Entertainment and has offered to purchase the 30 percent held by Usmanov's Red and White Securities firm, valuing the Premier League club at ?1.8billion.
Kroenke, owner of the Los Angeles Rams in the NFL, said having a single owner would benefit the club but fans said it was a "dreadful" day.
They have not won the title since 2004 and last season finished sixth, 37 points behind champions Manchester City.
Arsenal, who play City in their season opener on Sunday, are also adjusting to life after Arsene Wenger, who left the club in May after 22 years at the helm, replaced by former Paris Saint-Germain boss Emery.
"We at KSE are moving forward with this offer leading to 100 percent ownership of the club," Kroenke said in a statement published on the London Stock Exchange.
"We appreciate Mr Usmanov's dedication to the Arsenal Football Club and the storied ethos and history the club represents." Later on Tuesday, Red and White Holdings released their own short statement to confirm the deal.
"I wish all the best and great success to this wonderful football club and to all those whose lives and careers are entwined in it."
- Battle for Arsenal -
The deal brings to an end a battle between billionaires Kroenke and Usmanov for control of the club.
In October last year, KSE offered around ?525 million to buy the 18,695 shares held by Usmanov, the Russian businessman who himself attempted to buy out Kroenke in May 2017.
"The successful implementation of the offer will result in the opening of a new chapter in the history of the club in bringing 100 per cent private ownership by KSE," the statement said.
"KSE believes moving to private ownership will bring the benefits of a single owner better able to move quickly in furtherance of the club's strategy and ambitions. KSE is a committed, long-term owner of the club."
Kroenke has been a part-owner of Arsenal since 2007, gradually increasing his stake.
Under Stock Exchange rules, Kroenke will have to make an offer for the remaining minority shares in Arsenal, most of which are small numbers held largely by supporters of the club.
It is not currently mandatory for those shareholders to accept but if Kroenke purchases Usmanov's percentage, he can then push through a compulsory acquisition. This would see KSE take those final shares to complete a 100 percent takeover of the club.
The Arsenal Supporters' Trust issued a strongly worded statement opposing the move.
"Stan Kroenke taking the club private will see the end of supporters owning shares in Arsenal and their role upholding custodianship values," it said in a statement.
"The AST is also extremely concerned to note that this purchase is being funded by a loan," it added.
"The most dreadful part of this announcement is the news that Kroenke plans to forcibly purchase the shares held by Arsenal fans. Many of these fans are AST members and hold their shares not for value but as custodians who care for the future of the club."
Within two hours of the announcement '#KroenkeOut' was trending on Twitter in Britain.
Arsenal great Ian Wright tweeted: "Incredibly sad day for so many of our fan shareholders that no longer own a part of this club.
(This story has not been edited by Business Standard staff and is auto-generated from a syndicated feed.)