As expected, the Cheminots came into the match, defending in numbers as they had anticipated to frustrate the Sea Robbers and defend the 3-0 win recorded in the last meeting.
Abdeslam Ouaddou's men struggled to break their opponents' defence, and twice came close with Tshepang Moremi and Mbekezeli Mbokazi, respectively, but the duo missed the target.
On the other end, the meaningful attempt by Lupopo was from Basiala Amongo but Sipho Chaine denied him.
The Democratic Republic of Congo's outfit were eventually breached in the 39th minute as Masindi Nemtajela managed to beat the goalkeeper from about 25 yards to give Bucs a deserved lead.
Dramatic scenes after the game ended with Moremi getting his marching orders - though replays suggested it was harsh from the officials, alongside Christopher Sumbu, but the course of it all Dieumerci Mukoko, who head-butted a Pirates player, survived.
Bucs continued pushing after the break, with substitute Kabelo Dlamini proving to be a factor for them.
In the 50th minute, he forced the goalkeeper into a fine save, but his major contribution came in the 68th minute when he brought in a good corner that was converted by Yanela Mbuthuma to make it 2-0 for the afternoon.
The cheering Bucs fans' patience was rewarded in the final minute of added time, when Oswin Appollis managed to get the ball past the defenders infront of him and beat the goalkeeper to make it 3-3 and break Lupopo's hearts.
Much to the disappointment of the home crowd, Lupopo won the shootout 5-4 to get a ticket for the group stage.