The 23-year-old Smit, who placed third in the opening day individual time-trial, said he was pleased with his comeback after suffering serious injuries in a crash in France in April.
The RoadCover professional, who hails from Nelspruit, won the mountainous 140km stage in 3:53:24. Bell, also from Nelspruit, was awarded the same time.
Smit’s team-mate Mornay van Heerden, who set up the winning move, crossed the line in 3:53:42 to finish third on the day.
Bell leads the overall standings on 4:48:32 and will take a seven-second lead over Smit into the final stage. Van Heerden lies third on 4:49:33.
The stage, which started and finished in Nelspruit, took in the ascents of Spitskop and Long Tom Pass as it wound its way through White River and Sabie.
When the peloton ascended Long Tom Pass, a lot of riders were starting to sit on, said Smit.
“So I got Mornay to go really hard for the last two kilometres and the only rider who was able to follow us was Nico.
“The three of us rode away over the top and from there it was a matter of just rolling through once we were sure that we had a good gap,” said Smit.
“When we had a lead of about three minutes we started attacking Nico, but he had very good legs and it’s hard to ride away from someone when they are just sitting in your slip.
“But in the end we managed to win so it’s better than nothing.”
About 60km into the stage on Spitskop, the day’s first major climb, Smit’s team set him up for an attack that ultimately led to the demise of the yellow jersey.
Besides the lingering effects from his crash in the Tour de Bretagne, Smit said he was also fighting an upset tummy.
“I have been struggling with it throughout my career, so my form is dependent a lot on how I’m feeling.
“This is my first race in two months and when my nerves get too excited it often leads to stomach issues,” he explained.
“I’m usually on a good level but I’m not nearly where I should be. However, I have a great team behind me as usual and they are the foundation for my success.
“I managed to win today but I did not manage to ride Nico off as I was hoping to in order to collect the yellow jersey as well.”
Smit said he realised another tough stage lay ahead and that he would not gamble too early.
“If the stage starts easily I may have a chance to gain the seven seconds, but I will save my energy for Hilltop, which is one of the hardest climbs in South Africa.
“The summit is about five kilometres from the finish so if anything is going to happen it’s going to happen there.”
The third and final stage of the tour, which is presented by Rudy Project, is over 138km and features 3 100m of vertical ascent.
The elite women competed in today’s Bestmed Jock Classique, with Demacon’s Heidi Dalton ending on the top step of the podium after three tough stages totalling 154km.
Her winning time of 4:56:09 saw her take a close victory over Valencia’s Samantha Sanders (4:56:12), with her team-mate Carla Oberholzer (4:56:13) completing the podium.