The 37-year-old has not played for Australia since 2015 and has been brought in for Central Coast Mariners defender Kye Rowles who was ruled out with COVID-19 and Celtic's Tom Rogic who withdrew with injury.
Wilkinson will only feature in the squad for the Japan game at Sydney's Accor Stadium and is expected to act solely as cover for an injury.
Kuwait-based Ryan McGowan will replace Wilkinson in the squad for next week's game against Saudi Arabia in Jeddah.
The Socceroos are third in their qualifying group, three points behind Japan and have won just one of their past five qualifiers.
Football Australia is understood to have also considered bringing in Melbourne Victory's Matt Spiranovic and Melbourne City's Curtis Good.
Sprianovic has caught COVID-19 and City, who already have four players in the Socceroos squad, are understood to have rejected a request to release Good.
City were contacted for comment.
One of those City players is striker Jamie Maclaren who is unavailable for the game against the Saudis because he is due to get married.
The Socceroos were desperate to have Rogic on board and the initial signs from Celtic boss Ange Postecoglou were that the midfielder would be fit to play.
Instead, the 29-year-old will now remain in Glasgow in the lead-up to the Old Firm derby on April 3.
Victories in both fixtures should guarantee a direct passage to the World Cup in Qatar but the absence of Rogic represents a further hit to Australia's hopes of avoiding the play-off route.
The Socceroos were already without the services of Aaron Mooy, Riley McGree, Adam Taggart, Jackson Irvine and Harry Souttar until Rogic's withdrawal.
"Obviously it's a massive shame to not have those players around because they're very important to the squad and being a part of the journey the whole way," said midfielder Denis Genreau.
"It's a shame that he (Rogic) won't be with us for these games but we've got plenty of great players that can step up and do a great job."
Coach Graham Arnold apologised to the Socceroos squad on Tuesday after he was caught breaching NSW self-isolation protocols.
He has accepted a $25,000 fine by Football Australia.
Arnold, who tested positive for COVID-19 for the second time in two months, could still be on the touchline for the key clash with Japan provided he returns a negative result at the completion of his self-isolation period.
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