Shortly after seeing a header cleared off the line, the striker was not to be denied a second time and glanced in Tom O'Connor's cross for the only goal in their Group A encounter at Staplewood.
Dinamo's main threat came in the final 10 minutes but Southampton saw out the match to earn a second victory in as many Under-23 matches this season.
Southampton also face holders Porto and West Ham United in their group.
See: Southampton report
Southampton: 20 Aug v Stoke (A) PL2
Dinamo Zagreb: 13 Nov v West Ham (A) PLIC