The 61-year-old Setien, who was without a club since leaving Real Betis at the end of last season, has his first game in charge of Barcelona on Sunday, when the team hosts Granada in the Spanish League.
Don't be fooled into thinking that the Blaugrana are suddenly back, though. Whether you are first or fifth, you need to be fighting to be at the top, to win every competition.
Setien celebrated enthusiastically after the goal and on the final whistle, six days after replacing Ernesto Valverde at the Catalan club.
He practiced in Setien's first training with the main team on Tuesday and was followed closely by the new coach.
Marc-Andre ter Stegen returns in goal following a spell out with a knee injury, while the much-maligned Ivan Rakitic takes the place of the suspended Frenkie de Jong in midfield.
The Argentine turned it on as per usual, despite being brought down several times by a Granada defence looking to stop him at any cost. And in the second half Messi's low strike struck the side-netting.
Granada were soon on the back foot though as, after Antoine Griezmann had a shot saved, they were reduced to 10 men when defender German tripped Messi and received a second yellow card.
The defender was dismissed after 69 minutes and Barcelona were ahead by the 76th, with Messi coolly passing the ball into the net after an intricate team move.
Chased by La Liga giants to take over at Barcelona as a coach this past week, Xavi on Thursday cleared the air by saying at a media conference: "I will continue with Al Sadd at least until the end of the season".
Barca spoke to Xavi after their Supercup defeat to Atletico Madrid a week ago, but the midfielder, who is now coaching the Qatari club, Al Sadd, rejected the chance to replace Valverde.
"Not only great footballers, but those with whom I have worked with and who are honest, hard-working, good people".