The Paris Saint-Germain forward is facing charges of business corruption and could face two years in jail and a $9.7 million fine if convicted.
Frankfurt go through to the last four and the German club will now be eyeing a first European triumph since they won the UEFA Cup in 1980.
The 34-year-old football superstar has spent all his career at the Spanish club but he had been trying to make an exit since last year.
Karim Benzema put the champions in charge at a soggy Alfredo di Stefano stadium with a delightful backheel in the 14th minute while a deflected Toni Kroos free-kick doubled their lead in the 28th.
Laporta was last president at Barca between 2003 and 2010, which included overseeing the hugely successful appointment of Pep Guardiola as coach and the iconic treble-winning team of 2008/9.
The 22-year-old Kylian Mbappe's goals in the round of 16 first-leg tie made him the first-ever player to score a hat-trick against Barcelona in the knockout stages of the Champions League.
Barcelona Vice President Jordi Cardoner, however, denied the Spanish soccer club was in contact with Neymar amid reports the Brazil striker wants to leave Paris Saint-Germain.
Messi opened the scoring with an unstoppable free kick then combined with devastating effect with Luis Suarez to carve Betis open and score a second goal right before halftime.
European champions Real Madrid picked up a record fifth trophy of the year to cap a fine 2017 at the Club World Cup last weekend, but trail Barca by a mammoth 11 points at the top of La Liga albeit with a game in hand.
The five-times world player of the year agreed the new contract with Barcelona in July but the Catalan club did not release the usual photo of the player putting pen to paper, fuelling speculation he could depart in June 2018.
Barcelona's 100 percent start to the Liga season will be severely tested at Atletico Madrid in an atmosphere certain to be intensified by political fervour.
Neymar signed a new five-year deal with Barca in 2016, but the Catalans were powerless to stop his move to PSG just a year later.
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