Wits went down 2-1 on aggregate after losing 1-0 on Sunday afternoon, with Siyabonga Nhlapo given his marching orders for a foul on Toriq Losper in the box at Bidvest Stadium.
Nathan Paulse converted the penalty as the visitors booked a spot in the Final alongside holders Kaizer Chiefs, who edged Bloemfontein Celtic by the same scoreline last night.
Hunt bemoaned some of the decisions that went against his team, including in the first leg when Ajax goalkeeper Anssi Jaakkola escaped a red card three minutes in despite clattering Henrico Botes outside the area.
Hunt said: "Yeah look, over the two legs we never got the rub of the green did we? Some of the decisions killed us. Our red card was a red card, in the first leg they should have had a red card. In the first leg their goalkeeper should have been sent off.
"That is how football works. Obviously there was a hand-ball in the box [by Paulse on Sunday] and sometimes things don't go for you. But we still should have been better and good luck to Ajax."