Ashraf Mandela cancelled out Sharif Kimbowa's goal to ensure the Round of 16 tie with Wakiso Giants is decided through spot kicks after a 1-1 draw.
Alex Isabirye's tenure at Vipers started with the team's first goal in eight games and another penalty shoot-out in the Stanbic Uganda Cup.
Ashraf Mandela cancelled out Sharif Kimbowa's goal to ensure the Round of 16 tie with Wakiso Giants is decided through spot kicks after a 1-1 draw.
It is the third time in a row Vipers are going through a shoot-out in the cup competition, having beaten Bujumbura and Jinja North in the previous rounds.
The visitors started the game on the front foot and asked questions in the first half.
Paul Willa required a massive block to deny Martin Kizza inside the box as the Vipers controlled proceedings at the start of the game.
Bashir Sekajja dealt well with Kizza's goal-bound free-kick.
Yunus Ssentamu connected with Issa Mubiru's low cross from the left but was denied by the upright.
Ssekajja punched out Karim Ndugwa's powerful header from a Karim Watambala corner-kick, and the two sides went into the half-time break with no goals.
The home side was on top of things at the start of the second half and was rewarded when Marvin Nyanzi set up Sharif Kimbowa, who slotted home to put John Luyinda Ayala's side into the lead in the 47th minute.
Livingstone Mulondo was lucky to avoid putting the ball into his net off a Kimbowa cross as Wakiso searched for a second.
Substitute Norman Ojik was put through on goal by Nyanzi, but Fabian Mutombora well saved his shot.
Vipers needed to do something they had yet to do in the last seven games, scoring a goal in open play.
And it came from a rare source; Ashraf Mandela connected well with Kizza's cut-back to equalize for Vipers.
Substitute Abubakar Lawal came close to giving the visitors the lead, but Ssekajja punched away his header at the near post.
The home side had to negotiate the game's last minutes with ten men after Paul Willa was stretchered off injured.
Striker Desire Tety elbowed the defender.
The two sides could not be separated in regular time and went straight into the shoot-out.
George Kaddu sent Mutombora the wrong way to convert the first penalty and give Wakiso the lead in the shoot-out.
Ssekajja got a touch on Bright Anukani's spot-kick, but the power was enough, and Vipers levelled.
Rahmat Ssenfuka made it 2-1 through the middle, and Kizza levelled for the Vipers before Moses Aliro re-established the lead.
Lawal levelled at 3-3 before Ojik saw his weak penalty saved by Mutombora.
Hillary Mukundane converted Vipers' fourth, and that's all Vipers needed.
Tom Masiko hit the crossbar with Wakiso's last kick to send Vipers fans into a frenzy.
Stanbic Uganda Cup
Result
Wakiso 1-1 Vipers (3-4)