The fifth-wicket partnership was worth 67 in 15.3 overs before Steve Harmison found Agarkar's edge, Mark Butcher taking a good diving catch at third man.
Siddique, the 21-year-old left-hander, was eventually removed by Jacques Kallis, playing loosely outside off-stump to edge to wicketkeeper Mark Boucher.
And Hughes, 20, had a nightmare start, slashing at a short Steyn delivery off the fourth ball of the first over and only succeeding in getting a faint under-edge through to Mark Boucher.