Warner was due to play for Southampton-based Southern Brave.
The Aussie opener was drafted in by Southampton-based Southern Brave at a maximum fee amount of £125,000 ($249,000) for the first of its kind 100-balls per innings competition.
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Warner's withdrawal isn't likely to be last such instance of a cricketer pulling out of the event amid the growing threat of coronavirus pandemic.
James Erskine, Warner's manager, however, confirmed that the left-hander's decision is unrelated to the COVID-19 outbreak.
The 33-year-old has decided to make himself available for Australia's scheduled ODI series against Zimbabwe in August, which is part of the inaugural 13-team ODI Super League, beginning in May, working as the qualification pathway towards the next 50-over World Cup in India in 2023.
Zimbabwe's three-match visit down under is expected to be held at venues in Queensland and the Northern Territory, and will be clashing with a portion of The Hundred in England.
With the sport shut down across the globe, ECB's showpiece event is also under serious danger. However, the board is treating it as a priority by drawing contingency plans to ensure as much of the summer's profitable part can go-ahead in case the season is curtailed, which it most likely will be.
Apart from Warner, Steve Smith, Glenn Maxwell, Aaron Finch, Mitchell Starc and D’Arcy Short are other Australians that were signed up for the league on maximum wages, where as Chris Lynn, Nathan Coulter-Nile, Dan Christian and Adam Zampa also got deals.
(Inputs from Sydney Morning Herald)