Kroenke's offer values Arsenal at £1.8bn but is only slightly more than the offer Usmanov turned down only a few months ago.
United States-based investment vehicle Kroenke Sports and Entertainment said it received an "irrevocable undertaking" from Usamanov's Red and White Securities to accept the offer for its 18,695 Arsenal shares as soon as possible.
"I have chose to sell my shares in Arsenal Football Club which could be the best football club in the world", Usmanov said in a brief statement.
"KSE believes that taking Arsenal under private ownership will bring the flexibility necessary to drive greater success of the Club and intends to continue to develop the Club as a leading football club on both the domestic and global stage".
'I have chose to sell my shares in Arsenal Football Club which could be the best football club in the world, ' he said.
Red and White Holdings later released a short statement to confirm the deal.
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Although Usmanov's decision marks ultimate defeat for his consistently stated ambition to become the Gunners' majority owner, his profit on selling the shares will amount to around £300 million.
A "dreadful day" for Arsenal - fans' reaction While Kroenke says taking sole ownership will benefit the club, the Arsenal Supporters' Trust (AST) called the news "a terrible day" for the Gunners.
Kroenke is unpopular with some fans
"The Arsenal Supporters' Trust is wholly against this takeover", one fans' group said.
KSE's statement, which highlights Kroenke's ownership of various American football, basketball, ice hockey and Major League Soccer teams, insists his "commitment to Arsenal remains unwavering".
Within hours of the announcement the phrase '#KroenkeOut' was trending on Twitter in the UK.
The Gunners get their Premier League campaign underway on Sunday as they host champions Manchester City at the Emirates Stadium.
'We appreciate Mr Usmanov's dedication to the Arsenal Football Club and the storied ethos and history the club represents.
The motion, proposed by Brian Sedgemore MP, read: 'This House believes that Arsenal is the best club football team in the world at the moment and admires them for the fluency and poetry that they have brought to the lovely game'.
This would see KSE take those final shares to complete their 100 per-cent takeover of the club.
He was critical of Kroenke's passive ownership style, a sentiment increasingly echoed by Arsenal fans, unhappy with what they see as the board's willingness to settle for on-field mediocrity so long as commercial stability was maintained.More news: Turkish lira slumps to new record low as Donald Trump doubles tariffs
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