Coach Neil Powell has kept faith with his sevens specialists in naming a 12-man squad for next month's Rio 2016 Games, meaning Habana misses out along with fellow Springboks internationals Francois Hougaard and Ryan Kankowski.
Habana was one of many XVs stars hoping to switch to the shortened format as it makes its Olympic debut but, unlike fellow World Cup winner Sonny Bill Williams of New Zealand, he has not made the final cut.
The All Blacks star committed to the Sevens World Series early in the 2015-16 season, but Habana played at only two tournaments as he juggled his commitments with French club Toulon.
He said on his Instagram account he had appreciated just being part of the Blitzboks squad, which finished second overall behind Fiji, after a 12-year gap since his last sevens sojourn.
"I find myself incredibly fortunate to have become a part of a very special brotherhood, to have pushed myself further than what I had imagined in making the transition over to 7s, being helped each and every step of the way by all the members of the squad and getting to experience just how much love these boys have for each other," the 33-year-old said.
"Their hard work, dedication, commitment and never-say-die attitude is immensely infectious and will stand them in good stead as they head over to Rio to challenge for that gold medal.
"I'll be your biggest supporter and cheering you on loudly from Toulon!"
Habana, whose best 100 meters time is 10.2 seconds, famously raced a cheetah
and took on an A380 super-jumbo plane
as he capitalized on his reputation as one of rugby's fastest men.
Though he is not going to Brazil, South Africa has plenty of attacking potency, led by Seabelo Senatla. He was the leading try scorer in the 2015-16 series with 66 tries -- 18 more than second-placed American Perry Baker -- after also topping the standings in 2014-15 with 47.
Juan de Jongh is the only Springboks regular in the squad, while Hougaard is a traveling reserve.
Powell has called up 2015 World Sevens Player of the Year Werner Kok, who missed all of last season with injury.
"I could have picked three different teams and all would have been very competitive, but unfortunately, only 12 can go," Powell said.
"I want to thank all 23 players that contributed this year and the final 19 who really worked hard towards a common goal. That said, we are not done yet and will have to work hard in the remaining 20 days or so to fine-tune our play.
"We are not thinking medals, but rather on how to execute on our first match on day one of the tournament. We will focus on what we do well and that will hopefully bring the desired results."
Australia, which is drawn in South Africa's group for Rio
, also decided against taking Wallabies internationals when the squad was named Wednesday.
Nick Cummins and Henry Speight both suffered injuries which curtailed their chances, while Habana's Toulon teammate Quade Cooper was ruled out in May.
Jarryd Hayne is another high-profile sevens convert who has failed to win an Olympic place.
The former Australia rugby league star cut short his NFL contract to join up with Fiji for May's series finale in London, but he has not made it to the last week of the team's selection camp.
Coach Ben Ryan said last weekend that Hayne, although committed 100% to the program, had not had enough time to catch up with more established members of the squad.
"He added hugely to the squad with his attitude off and on the field and I have no doubt this has improved everyone's performance levels and helped the team in their pursuit of Olympic success," said Ryan, who will name his 12-man squad on Saturday.