The qualifying event in late June was scheduled to take place in Taiwan, but was moved to Mexico after the Taiwanese government restricted foreign arrivals in the face of an outbreak.
“We worked on several options and scenarios, but the logistical challenges of providing a safe environment for the group were overwhelming,” said Williams.
“Even though Team Australia managed to win the event, timing did not allow the team to complete quarantine in Australia and meet entry requirements for the Tokyo games.
Chinese and Chinese teams in Tapei have also withdrawn from Olympic qualifiers, according to Baseball Australia.
Baseball returns to the Olympics for the first time since Beijing 2008. Australia won a silver medal in baseball at the 2004 Athens Olympics.
Japan, Israel, Mexico, South Korea and the United States have already qualified for the Tokyo Games baseball event, with the Dominican Republic, Venezuela and the Netherlands vying for last place in the tournament qualifier from Mexico, to be held on June 22. 26 in Puebla.
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