Nyasha Mushekwi was the hero for the Brazilians, turning home Matty Pattison's shot on the half-hour mark.
The visitors had all the play for the opening 15 minutes, but it was Vasco who had the first chance of the night when Jonathan Armogam shot weakly at goal after being nicely set up by Sibusiso Zuma’s square ball.
Mushekwi had Downs’ first chance of the night, but saw his goal-bound 21st-minute volley smash into Aiden Jenniker when a goal seemed a near certainty.
Despite finally having started to enjoy more of the ball, Vasco found themselves 1-0 down in the 29th minute when Pattison’s diagonal shot across the goal was neatly buried at the back post by Mushekwi.
That was it for first half goal-mouth action; the next chance arriving three minutes into the second stanza when Armogam skied a close-range volley after some great work by Jenniker.
In the 56th minute a moment of hesitancy from Calvin Marlin allowed Armogam to steer the ball over his head towards the net, but Vuyo Mere saved the day for Downs right on the goal-line.
Vasco showed they could really match their more illustrious opponents as the game remained tight; the next chance coming in the 80th minute when Bradley August came close with a 30-yard free-kick.
Downs had a couple of half-chances late on through Mabuthi Khenyeza and Franklin Cale, and in the end managed to hold on to a hard-earned win against the Cape side, who made a real game of it in the second half with superb endeavour.