The Jamaican 2011 World champion was involved in a photo-finish with Nigerian Seye Ogunlewe before being awarded the bronze in 10.19s.
Bronte Campbell denied her older sister Cate a fourth gold of the Games, taking the honours in the 100m freestyle final in a Games-record 52.27secs.
Blake was still in the picture for the silver but was overtaken by a strong finishing Jies, who clocked 10.17s.
Bolt, who retired previous year with eight Olympic golds including two 4×100 relay titles shared with Blake, tweeted his congratulations to his team mate and Simbine.
"After the 100m yesterday I felt happy with it but I felt media-wise it was a bigger deal that I didn't get gold, that it wasn't an achievement to win silver", she said.
"I got out and didn't see anyone".
Stella Chesang fought off Kenya's Stacy Ndiwa to take the 10,000m gold for Uganda and win her maiden Commonwealth medal.
It was quite apt that Bruintjies and Simbine shared the podium as they have been at the forefront of South African sprinting the last four years.
Earlier in the day, England's world indoor champion Andrew Pozzi qualified fastest for Thursday's 110m hurdles final, while team-mate and London 2012 bronze medallist Robbie Grabarz, competing at the Commonwealth Games for the first time at the age of 30, advanced to the high jump final by clearing 2.21m at his second attempt.
"I am quite happy with the performance, for a couple of years I've been working hard but I haven't been in finals like Akani", Bruintjies said. "I just focused on myself".
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Simbine, smiling broadly, said that he was "humbled" by victory.
"Maybe I was too confident and over thought it", said Blake, who appeared to be uncharacteristically quiet behind the blocks.
In swimming, Cameron van der Burgh of South Africa stunned England's Adam Peaty, the world record-holder, to defend his 50 metres breaststroke title.
"It's my first worldwide title and for me it's a milestone, a stepping stone towards the world championships, and the Olympics and more competitions and more global competitions", said the 24-year-old.
Earlier, bowls quartet Elma Davis‚ Esme Kruger‚ Nicolene Neal and Johanna Snyman won South Africa's second medal on the greens at the Games.
Visibly disappointed with bronze, Blake seemed to have no idea that he was fortunate to have won a medal at all.
Their silver medal pushed South Africa's tally at the Games into the double figures winning the country's 10th medal.
Tomas Walsh did not match his Games record 22.45 metres in qualifying but was still a comfortable victor in the men's shot put final.
The Jamaicans had already missed out on gold in the women's 100m final, which went to Michelle-Lee Ahye of Trinidad and Tobago.