The two teams could not be separated in 120 minutes, with an own goal from Gianluca Mancini cancelling out an opener from Paulo Dybala, but Sevilla were triumphant in the penalty shootout, with Gonzalo Montiel winning it for the Spanish outfit after a retake.
Jose Luis Mendilibar's side will play Champions League football next season despite a disappointing La Liga campaign, which has left them down in 11th spot in the table, while Roma are currently sixth in Serie A ahead of the final matchday, which would see them qualify for the group stage of the 2023-24 Europa League.
The trophy is Sevilla's seventh in this competition, with Los Nervionenses also triumphing in 2006, 2007, 2014, 2015, 2016 and 2020.
Roma's goalless draw away to Bayer Leverkusen in the second leg of their semi-final, which saw the Italian outfit win the tie 1-0, was peak Mourinho, with the Portuguese setting up to frustrate the Bundesliga side, but it just was not to be for the Serie A side on Wednesday.
The fact that Sevilla beat Manchester United and then Juventus in the quarter-finals and semi-finals demonstrates the impressiveness of their position in the final, and it has been some turnaround for the club since Mendilibar's arrival, with the 62-year-old taking over a relegation-threatened side in La Liga.
Roma had the final's first chance in the 11th minute, when smart work from Dybala and Zeki Celik eventually led to Leonardo Spinazzola having a strike on goal, but Bono was on hand to make a smart save.
Sevilla were enjoying more of the ball in the early exchanges, but Roma's threat on the counter-attack was obvious, and Bono had to vacate his goal in the 12th minute to clear ahead of Tammy Abraham.
Oliver Torres sent a wayward effort wide of the Roma goal in the 25th minute during a period when the contest had become scrappy, with the referee intervening due to a number of late tackles, and it was Nemanja Matic that picked up the first booking of the contest following a challenge with Lucas Ocampos.
Roma wanted a penalty in the 31st minute, with Abraham going down under a challenge from Nemanja Gudelj, but the referee was happy for the play to continue and VAR agreed.
The breakthrough arrived three minutes later, and it was Dybala with the goal, with the Argentine gathering a incisive pass from Mancini before finding the back of the net.
Sevilla came incredibly close to levelling in the latter stages of the first period when Ivan Rakitic struck one from distance, but the midfielder's effort crashed off the base of the post.
The holders were much improved at the start of the second half, with Alex Telles just missing the target in the 52nd minute, and the La Liga outfit then managed to level the scores three minutes later.
A smart team move ended with Jesus Navas delivering a dangerous cross into the penalty box, and the ball bounced off Mancini and into the back of the Roma net for 1-1.
Abraham should have sent Roma back ahead in the 67th minute when he met a knockdown inside the penalty box, but the striker somehow fired straight at Bono, before Roger Ibanez turned wide from the rebound.
Sevilla were initially awarded a penalty in the 76th minute when Ocampos went down inside the box under a challenge from Ibanez, but referee Anthony Taylor overturned his decision after looking at the monitor.
Roma had a penalty shout of their own in the latter stages when a strike from Spinazzola hit Fernando's arm, but the referee said no, much to the frustration of the Italian side's bench, before Andrea Belotti had a shot turned wide of the post by Bono from inside the box.
It was no surprise that the contest headed for extra-time; Sevilla actually had a couple of late chances to win it in normal time through Youssef En-Nesyri and Fernando, but Roma managed to keep the score 1-1.
Chris Smalling crashed a header against the Sevilla crossbar in the final stages of extra-time, but neither side did enough in the additional 30 minutes to deserve to triumph through that avenue, so it was left to a penalty shootout to determine the winner of the exhausting contest.
Ocampos sent Sevilla ahead in the shootout before Bryan Cristante levelled, but Erik Lamela then made it 2-1 to the Spanish outfit with a cool penalty into the bottom corner.
Mancini saw his effort saved by the legs of Bono, before Rakitic sent Sevilla 3-1 ahead; Ibanez then missed for Roma, hitting the post, handing the Spanish outfit the chance to win it; Montiel's initial penalty was saved, but a retake was ordered by VAR, and he converted on the second occasion to secure a 4-1 success in the shootout.