However, it was far from a perfect evening for the Catalans as Neymar had to be carried from the field after suffering a nasty looking right ankle sprain midway through the first-half.
Barca boss Gerardo Martino, though, played down fears that the Brazilian could be sidelined for a significant period of time.
"We don't think it is as bad as it appeared on television. He could be out for a period of time, but it shouldn't be too serious, the player is fine," he said.
With his side already leading 4-0 from the first-leg, thanks in part to two goals from Messi on his first appearance as a substitute after two months out, Martino made nine changes to the side that started Saturday's La Liga 0-0 draw at Atletico Madrid.
Neymar was also making his first start of the year after recovering from a bout of gastroenteritis.
However, his return lasted only 23 minutes as he had to be helped off the field by two members of the Barca medical staff as he turned his ankle in attempting to cross the ball from the left side of the area.