The Sea Robbers found themselves 2-0 down inside the opening 10 minutes but did well to level matters and go into the half-time break with the scoreline at 2-2.
Alfred Ndengane then fired Pirates ahead in the second half, only for Cape Town City to make it 3-3 in the dying minutes of the game.
"We started a little bit shaky. We go 1-0 down, [and] we're still shaky again. We go 2-0 down against the run of play, a little bit, we tried to find our feet again and a bit of emotional stability which we struggled with at the beginning of the match," Mokwena told SuperSport TV.
"Once you're 2-0 [down], you go a little bit and show character. We were the better team by far after the first 15 minutes. We should have won the match. I need to see the last action clearly. I don't know, maybe we need VAR," he said.
Mokwena felt his side should have been awarded a penalty in the closing stages of the match after Thabiso Monyane appeared to be fouled.
"If he comes from behind like that and Thabiso [Monyane] is in front of the ball, and is in control and inside the box, well, I'm not in charge of the referees. I don't talk about refereeing decisions to be honest. We focus on trying to improve the team. We can't control those situations."
"The positives are that we fought. Orlando Pirates fight. We fought a very serious battle against a very good team. We were the strongest of the two teams on the pitch after 20 minutes. We need to work on managing critical phases. 3-2 with 10 minutes to go, we should be able to close shop and see the game out."
After being shown the incident during his interview, Mokwena said: "Everyone sees it for themselves, I don't have to comment about it, everybody sees, unfortunately. No comment, everybody can see."