Makarenko completed the distance in 13.55 seconds, with Shubenkov just 0.15 seconds behind. China's Zhang Zizijun finished third at 0.24 seconds after the leader.
In the women's 100-meter hurdles, Belarus's Elvira Graborenko claimed victory with a time of 12.81 seconds, followed by Russia's Viktoria Pogrebnyak with 13.13 seconds and another Belarusian, Svetlana Parahonko on 13.15 seconds.
The BRICS Games are being held from June 12 to 24, with around 5,000 athletes from more than 90 countries competing in 387 medal events.