Stander, 24, left the Blues to join Munster in 2012 and has played a key role in helping them to second place in the RaboDirect PRO12 this season with two rounds remaining.
Having not been capped by the Springboks, will find himself eligible to play for Ireland next year.
And Habana believes the Springboks let the former South Africa Under-20s back row slip through their net.
"Someone like CJ has used the opportunity to come overseas, and take off from where he left off as a youngster within South Africa, and he has really done well," Habana told the Belfast Telegraph.
"It will be a loss but whatever the loss to South Africa it will continue to be Ireland's gain.
"There have been a couple of players who have gone on to represent other countries extremely well, not only in Europe but around the world.
"CJ is a very talented player, he showed a lot of potential and promise as a youngster.
"It was sad to see him leave South Africa, and the Bulls did their utmost to keep him."
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Guinness PRO12 Munster News
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