Habana and fellow Springbok Schalk Brits were named in the South African sevens team for the Games but both were denied a chance to play by their respective clubs.
Toulon had a change of heart on Tuesday but the decision came after the deadline for the submission of squads for the Games had expired, the South African Sports and Olympic Committee said in a statement.
As a result, the leading scorer in Springbok history is unable to join the team preparing in Glasgow unless there is a late injury to another players.
South Africa's rugby sevens team opens their competition on Saturday with group games against Trinidad and Tobago, the Cook Islands and Kenya before the knock-out matches and medal games on Sunday.
(Reporting by Mark Gleeson; Editing by Amlan Chakraborty)
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