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Jobodwana won the 200m race, ahead of Steven Colvert from Ireland (20.57sec), with Jamaican Ainsley Waugh finishing in third (20.58sec).
South Africa's Wayde van Niekerk competed in the same race and finished fifth overall (20.91sec), behind Britain's Daniel Talbot in 20.71sec.
Jobodwana's first qualifier was at the Mississippi Open in Oxford, USA on April 14 where he clocked a fast 20.32sec run, ranking him the fastest athlete in South Africa this season.
The 19-year-old came third at the SA Junior Championships in 2010 and is currently ranked number 18 in the world.
Elroy Gelant won the men's 5 000m ahead of Abdi Naeeye of the Netherlands and Brazil's Joilson Da Silva.
Gelant did not reach the qualifying standard of 13:20:00, with the clock reading 13:46.17 as he crossed the line.
Nageeye and Da Silva clocked 13:58.11 and 13:58.89 respectively.
In the men's 800m race, South African athlete Johan Cronje finished second behind Slovenia's Zan Rudolf, with Morocco's El Amine Mouchine crossing the line just after Cronje in 1:46.93.
Ruan Greyling finished fourth in the men's 400m, clocking 46.55sec.
Patience Ntshingila, Claudia Viljoen, and Estie Wittstock were among the South African women who competed in Sweden.
Wittstock - in the 400m event - crossed the line in 52.99sec behind Italian national champion Maria Spacca (52.73sec).
Claudia Viljoen finished 10th overall in the women's 100m hurdles in 13.84sec.
The winning time was 13.11sec by Beate Schrott of Austria.
