The action-packed, all-Spanish match was won when Pedro, linked by British media with a move to Manchester United, scored from close range after a shot by Messi rebounded in the 115th minute.
In the final seconds of extra time, Sevilla defender Adil Rami had a golden chance to send the match to penalties but missed an open goal from close range.
Earlier, Sevilla had battled back from 4-1 down to 4-4 as Barcelona’s fitness was tested in its first competitive match of the season – Europe’s curtain-raiser between the winners of the Champions League and the second-tier Europa League.
“I thought we were much better, much stronger,” Messi said of the first hour of the match. “We had the ball for the first 60 minutes, we had opportunities, we scored. And then we seemed to have relaxed, we let them have the ball, we withdrew a bit.
“It got pretty tough when we looked like we were winning hands down, but fortunately we didn’t have to go to penalties.”
Calling the match “spectacular” for Barcelona’s supporters, coach Luis Enrique suggested his team had taken too many risks while leading.
“We’d practically closed the match, but it’s very difficult to secure this,” he said. “When you’re winning 4-1, the rival has got nothing to lose. What we do need is to analyze what happened at that point and the risks that they took.”
Luis Enrique refused to discuss whether Pedro’s winning goal could make it more likely for him to stay with the club.
His Sevilla counterpart Unai Emery said he was “very proud” of his team, which has been rebuilt over the summer after its Europa League win.
“If there’s one thing we want to make this team, it’s competitive. We want this team to really go for victory whatever the circumstances,” he said. “We stood up to the best team in the world.”
On a warm summer night, Barcelona was without injured left-back Jordi Alba and star striker Neymar, who is ill with mumps, while various absences for Sevilla meant that midfielder Grzegorz Krychowiak dropped into the center-back role.
European champion Barcelona went behind three minutes into the game when Ever Banega scored from a free-kick from the edge of the penalty area.
Messi curled two direct free-kicks past Sevilla goalkeeper Beto in the seventh and 16th minutes and was a constant threat in attack with throughout the first half, though he made less of a mark after the break.
Barcelona’s third came shortly before halftime when Luis Suarez pounced on the rebound after his shot was parried by Beto and crossed for Rafinha to score.
Suarez grabbed a goal in the 52nd minute following a poor pass by Sevilla defender Benoit Tremoulinas. The French left-back gave the ball away to Sergio Busquets, who played in Suarez to apply a calm finish. However, it was canceled out almost immediately when the unmarked Jose Antonio Reyes ran in at the far post to steer home a cross by Vitolo.
Vitolo was again in the thick of the action a quarter of an hour later as he tried to reach a cross from Tremoulinas but was fouled by Jeremy Mathieu, playing at left-back for the injured Alba. The resulting penalty was hit hard and left by Kevin Gameiro.
Sevilla pulled level when debutant Yevhen Konoplyanka slotted in from close range off a low pass from Ciro Immobile in the 81st minute.
Having won the Spanish league and cup titles, along with the Champions League, lifting the Super Cup keepsBarcelona on track to win six trophies in a calendar year, a feat the club last achieved under Pep Guardiola in 2009.
Next up is the Spanish Super Cup against Atheltic Bilbao on Friday and Monday, before the Club World Cup in December.