With scores locked at 1-1 in the 53rd minute, Vukovic attempted to intercept a cross but was connected by his own teammate in the process with Prague going on to prod the ball home with Vukovic down in clear pain.
The 33-year-old would need to be stretchered from the field and was replaced by Komaan Nordin in goal, who couldn't prevent Slavia running out 4-1 winners.
It's currently unclear the exact nature or extent of the injury, though replays suggest a rib or torso injury.
Vukovic had only just secured a two-and-a-half-year contract extension with Genk this week having impressed since joining from Sydney FC in 2017.
Genk are currently eight points clear at the top of the Belgium first-division and haven't won the title since 2011.