An afternoon of drama saw the Cape side throw away a two goal lead, but the hosts finally triumphed 5-4 in the penalty shootout, during which five spot-kicks were saved.
Bucs had the lion's share of goal chances in the first half and also had several corners, but were unable to convert any of the opportunities that came their way.
A 12th minute corner from Joseph Makhanya located Gilbert Mushangazhike at the back post, but the Zimbabwean did not time his jump correctly and his header sailed high over the bar.
In the 17th minute Pirates launched a sweeping attack down the right flank. Joseph Makhanya's quality cross set up Excellent Walaza perfectly, and while the young striker connected well from 12 yards out, Roberts did brilliantly to make the block.
Four minutes later Santos looked certain to open their account when a fantastic through-ball by Tawonga Chimodzi released Erwin Isaacs through on goal, only for Bucs keeper Senzo Meyiwa to pull off a stunning save from just six yards out.
From the outset the match had been a physical affair with challenges flying in from both sets of players.
While referee Ace Ngcobo initially kept his cards in his pocket, the latter stages of the half saw his brandishing a few yellow cards. Then, in the 39th minute, he was given little choice but to show a straight red after a scything challenge by Lucas Thwala.
The Peoples' Team took immediate advantage as they scored from the resultant free-kick as Musa Otieno guided Isaacs' cross into the net, beating Meyiwa at the near post.
It took just four second half minutes for the Cape side to extend their lead, courtesy of a special goal by Ryan Chapman.
The young striker picked the ball up near the edge of the area before sending a rocket of a shot with his left foot into the top corner, giving Meyiwa no chance.
Santos continued to push forward and Meyiwa did well to deny well-struck efforts by Marvin Oakes and Thembile Kanono.
But, somewhat against the run of play, Pirates managed to halve the deficit when Kanono brought down Modise in the box. The Bafana Bafana midfielder converted the spot-kick himself, clinically putting the ball past Roberts in the 60th minute.
The goal saw the large Pirates contingent of fans in the stadium come to life, which immediately lifted the Buccaneers' game and completely changed the complexion of the match.
In the 72nd minute Walaza was put clean through on goal and the equaliser seemed imminent, but Roberts saved brilliantly to keep his team in the match.
But the pressure from the Soweto giants was relentless and they levelled matters in the 79th minute when Bennett Chenene glanced home Modise's free-kick.
By this stage of the game it was all Pirates. While Santos did well to hold on until extra time, their cause was not aided when Kanono was sent-off after picking up a second yellow card.
The fast pace of the game did not let up in extra time and in the first minute of the additional period Pirates wasted a great chance when Chenene blasted over from five yards out.
The action quickly reverted to the other end of the field, where Santos had several chances to score, but found Meyiwa to be inspired form as he frustrated Rodgers in particular.
In the 105th minute Marvin Oakes was given the chance to make a hero of himself, but his shot flashed just wide of goal.
The relentless pace of the game finally seemed to catch up with the players in the second half of extra time and neither side really came close to grabbing the winner, with the exception of a Rodgers shot which flashed wide of goal, and a late header from the same player, which was saved by Meyiwa.
Sebastian Bax and Musa Otieno both had their penalties saved by Meyiwa, but Roberts, who had been outstanding throughout the game, denied Lebohang Mokoena, Teko Modise and Lindokhule Mkhanazi, to win the game for Santos after a thrilling two hours of football.
Penalty sequence: Santos shoot first – Isaacs scores 1-0, Mokoena misses (saved Roberts) 1-0; Rodgers scores 2-0, Chenene scores 2-1; Bax misses (saved Meyiwa) 2-1, Mdledle scores 2-2; Gabonamong scores 3-2, Modise misses (saved Roberts) 3-2; Otieno misses (saved Meyiwa) 3-2, Mushangazike scores 3-3; Chapman scores 4-3, Walaza scores 4-4; Arendse scores 5-4, Mkhwanazi misses (saved Roberts) 5-4.