The Spanish and European champions were leading 2-1 from the first leg in Bilbao last Sunday and Messi's superbly-taken opening goal early in the second half snuffed out any hopes of an unlikely Athletic comeback at a packed Nou Camp.
The Argentina forward picked up a pass from new signing Zlatan Ibrahimovic in the 50th minute, rounded an Athletic defender and from close to the byline clipped the ball over onrushing goalkeeper Gorka Iraizoz.
His second came from the penalty spot after Daniel Alves was felled and Krkic made sure of Barca's first trophy of the season when he intercepted Ander Iturraspe's mis-hit backpass, rounded Iraizoz and stroked the ball into the empty net.
Pep Guardiola's side have a chance of winning five more trophies this season and play UEFA Cup winners Shakhtar Donetsk of Ukraine in the European Super Cup in Monaco on Friday.
They are also contesting the domestic championship, the UEFA Champions League, the King's Cup and the FIFA Club World Cup.
The Super Cup is Spain's traditional season opener between the winners of the league and King's Cup. Barca won both last season, beating Athletic 4-1 in the final and have now won eight Super Cups, equal with Real Madrid.
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