Messi opened the scoring in spectacular fashion by dribbling past four Athletic players and lashing home a low finish before Neymar added a second before half-time.
The Argentine grabbed his second of the game to kill the tie as a contest 17 minutes from time before Inaki Williams grabbed a consolation for the Basques.
Despite Athletic fans dominating two-thirds of the 99,000 capacity Camp Nou, there was nothing their players could do to stop a rampant Barca that is now just one game away from just the second treble in the club’s history.
Luis Enrique’s men face Italian champions Juventus in the Champions League final in Berlin on June 6.
“From the start we saw a great Barca with all the players at a high level,” said Barcelona boss Luis Enrique.
“It is a shame for Athletic to have played these finals in the last few years against a Barca playing so well.
“They deserve a Cup and I hope they soon get it because the behaviour of their fans was spectacular.”
The game began in controversy after the Spanish national anthem was drowned by the fans of two clubs with strong separatist identities.
– Heavily involved Messi –
On the field there was little to argue about as Messi tore Bilbao apart to continue their 31-year drought without winning a major trophy.
“He is a player that we always say appears in the most decisive moments and obviously he wasn’t going to miss out in a final,” said Athletic coach Ernesto Valverde.
“His first goal was incredible.”
The four-time World Player of the Year teed up Neymar for what should have been the opening goal just nine minutes in, but the Brazilian’s effort was wrongly disallowed for offside.
Luis Suarez then forced Iago Herrerin into the first of many fine saves with a low drive.
Herrerin was left as helpless as the rest of his teammates 11 minutes later when Messi danced past Mikel Balenziaga, Mikel Rico and Benat Etxebarria tight on the touchline before turning inside Aymeric Laporte and smashing in at the near post.
Even by the Argentine’s incredibly high standards the move and finish was as good as any of his previous 410 Barca goals.
Messi wasn’t finished as he then turned provider for Suarez whose low cross was met by Neymar and brilliantly blocked by Herrerin.
The Athletic stopper continued to frustrate Barca as he then stretched to turn Gerard Pique‘s effort from Messi’s free-kick over.
Barcelona did finally double their advantage nine minutes before half-time with Messi again heavily involved as he fed Ivan Rakitic who released Suarez and this time the Uruguayan’s pass was rolled into an unguarded net by Neymar for his seventh goal of the competition.
Athletic starlet Inaki Williams came closest to a reply before the break with a dipping volley that clipped the top of the crossbar.
However, Herrerin had to be alive moments later to turn a free-kick from Messi behind.
Perhaps with one eye on next weekend’s Champions League final, Barca eased up slightly in the second period.
Xavi Hernandez was brought on to savour his final appearance at the Camp Nou after a 17-year career.
Messi added his 58th goal of the season as he pounced on some lackadaisical Athletic defending to prod home Dani Alves‘s cross.
The Bilbao faithful did at least get something to cheer 11 minutes from time as the 20-year-old Williams notched just his third senior goal from Ibai Gomez’s cross.