Lance Niewenhuis made a save to deny Rudzani Ramudzuli in the penalty shootout and Tonic Chabalala missed his penalty. Beaford Tshabalala missed his penalty for United.
Both goals were scored in extra-time, the Pirates goal was scored by Lucky Lekgwathi and the equalizer came from Bernard Parker.
The first half was dominated by Pirates with them having almost all the scoring opportunities but United did get more into the match during the second half and threatened the Pirates goal but overall Pirates should have won with all the good scoring opportunities they had.
United lost striker Serge Djiehoua, early in the half, due to an injury to his leg after a clashing with Paulos Masehe. He was replaced by veteran Clement Mazibuko.
Teko Modise had a few attempts at goal but missed the target with a free kick over the bar and was also denied by keeper Lance Niewenhuis.
Mazibuko came close to scoring in the 31st minute when is free kick sailed narrowly over the bar.
A minute later United had a chance but Katlego Loke hammered his shot over the bar.
Jorry Merahe nearly opened the scoring for Pirates when his shot from outside the box went narrowly past the upright in the 39th minute.
Ryan Botha had his shot easily saved by Francis Chansa in the 53rd minute.
In the 66th minute Modise hammered a long-range shot that went narrowly past the post.
Chansa made a great diving save in the 72nd minute to deny Sibusiso Zwane from scoring with a well struck shot from outside the box.
Five minutes later both Modise and Lehlohonolo Seema had shots blocked by the defence.
In the 89th minute Pirates nearly got the winner but Beaford Tshabalala saved United by heading the ball off the goal line.
The match went to thirty minutes of extra-time after the sides were tied at 0-0 after 90 minutes.
In the 92nd minute Pirates took the lead when Lucky Lekgwathi scored with a header from a corner taken by Bennett Chenene.
United got a late equalizer in the 113th minute when a Bernard Parker shot took a deflection off a Pirates player to beat Chansa and go into the goal.
The game ended 1-1 after extra-time and went to a penalty shootout.
United won the penalty shootout 5-4 to go to the next round.