Israel and Hamas blame each other as Netanyahu rules out the group's demand for an end to the war in exchange for the freeing of hostages
A Luis Suarez volley put Barca ahead in the 35th minute while Brazil international Neymar earned and converted a penalty three minutes into the second half to score his first goal since October and put Barca in front in the tie after losing the first leg 2-1.
Athletic responded immediately though, substitute defender Gorka Elustondo crossing for Barcelona-born Enric Saborit to head home in the 51st minute. The goal emboldened the visitors for a 10-minute spell but Barca withstood the pressure.
Messi had squandered two free kicks in the first half but avoided the possibility of extra time and penalties by curling a dead ball in off the post in the 79th, his second set piece goal in four days.
"We didn't lose our composure, we created lots of chances and I think we deserved to go through," Barca coach Luis Enrique told reporters after a first win in 2017 following the defeat in the first leg and Sunday's 1-1 draw with Villarreal.
"We controlled the game today and Athletic practically had no chances."
Barcelona had been livid with the referee's decisions in the first leg after Gerard Pique and Neymar were denied penalties and Bilbao's Aritz Aduriz was fortunate not to be shown a red card.
The Nou Camp exploded with rage on Wednesday when Neymar was harshly ruled offside as he squared for Suarez to find the net.
Barca channeled their sense of injustice to craft a brilliant opening goal, however, Messi wriggling free of two players in midfield to slip the ball to Neymar who turned his marker and crossed for Suarez to acrobatically volley home.
It was the Uruguayan's 100th goal for the club since joining from Liverpool in 2014.
Barca struck again at the start of the second half when Neymar cut into the area from the left and danced past one defender before falling over the body of Eneko Boveda and winning a penalty.
The Brazilian coolly converted to score for the first time since the 4-0 win over Manchester City on Oct. 19.
Neymar hit the post later as Athletic grew tired and the Basques were condemned to another cup defeat at the hands of Barcelona, who beat them in the final in 2009, 2012 and 2015 and sent them packing in the last eight last season.
Barca join Alaves, Alcorcon, Atletico Madrid and Real Sociedad in the quarter-final draw which takes place on Friday, with Real Madrid, Eibar and Celta Vigo, who all take heavy advantages into their second-leg games on Thursday, aiming to join them.
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