The Clever Boys netted as early as the seventh minute through veteran midfielder Dillon Sheppard.
They doubled that lead on 25 minutes, with Sibusiso Vilakazi this time finding the back of the net.
It took a while before the back of the net was found again, but it eventually happened on the hour-mark when defender Markus Lecki finished from a corner.
The Students also held a 3-0 first leg lead last year against Royal Leopards of Swaziland before letting it slip, but will be confident of getting the desired result at home against Lightstars in the second leg.