Jamaican Olympic champion and world record holder Usain Bolt grabbed gold in 19.55 seconds, with his American rival Justin Gatlin settling for silver in 19.74.
Jobodwana, who hails from King William's Town, snatched his podium spot by two thousandths of a second in 19.87.
In the process he set a new personal best just a day after clocking 20.01 in the semi-finals.
Madibaz athletics manager Nellis Bothma said Jobodwana had done the club proud.
The previous national record of 19.94 was held by Wayde van Niekerk, who claimed gold in the 400m the previous day.