The victory came hours after reports made rounds that head coach Alex Isabirye would step down from his role after the game.
Joint-record winners Express needed post-match spotkicks to tame a resilient Rwenzori Lions in the Round of 32 of the Stanbic Uganda Cup.
The Red Eagles edged their visitors 8-7 after it had ended 1-1 in the normal 90 minutes.
13:43 - 17.02.2024
Reports: Shocking turnaround as Isabirye's future at Express is doubtful, again
From an imminent departure after last Saturday's 4-3 Uganda Premier League defeat to KCCA FC to reports of staying, it's back to "Isabirye to leave" within a space of just a week.
Striker Isaac Wagoina forced the game into penalties in the latter stages through a penalty, after Express were headed for a shock exit from the 50th edition of the competition.
The victory came hours after reports made rounds that head coach Alex Isabirye would step down from his role after the game.
18:08 - 17.02.2024
Stanbic Uganda Cup: KCCA's pursuit for a record trophy going to plan
The Abdallah Mubiru-coached side are looking to find solace in the Cup for glory this season, as the Uganda Premier League seems out of reach.
In the other game on the day, URA FC smiled to a 2-0 win over Kumi Unite at the Boma Grounds.
Attacker Moses Aliro and youngster Amisi Bwangani scored for the Tax Collectors in the Far East to reach the Last 32.
16:32 - 16.02.2024
Stanbic Uganda Cup: Kitara dump Gaddafi to sail into the Last 16
Forwards George Ssenkaaba and Denis Omedi were on target for the Royals at the Masindi Municipal Stadium to eliminate the Soldier Boys.
However, the latter was forced to withdraw prematurely, having suffered a bad injury, with David Obua's team finishing the game with ten players.