Leverkusen were guilty of missing several good openings in the second half especially by Hakan Calhanoglu when a win would have seen them through to the next round.
However, the draw meant they finished third in Group E level on six points with AS Roma, who were held 0-0 by BATE Borisov, but eliminated due to a poorer head to head record.
Last season’s treble winners Barca are in the knockout stage for the 12th successive year and finish with 14 points from their six matches.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
Barca coach Luis Enrique could afford to rest players ahead of the Club World Cup later this month and made eight changes from the side that drew with Valencia in La Liga on Saturday.
Still there was a place for Messi who is rediscovering his top form after a knee injury that kept him sidelined for almost two months.
Leverkusen pressured with raids from Admir Mehmedi down the right wing and a dangerous free kick from Calhanoglu was parried well by keeper Marc-Andre ter Stegen.
A defence splitting pass from Ivan Rakitic found Messi who rounded keeper Bernd Leno and put Barca ahead, but Leverkusen quickly responded with Hernandez sweeping home after a Mehmedi cross found him in the centre of the penalty area.
The chances built up for Leverkusen in the second half with Ter Stegen saving well, especially from Calhanoglu and Mehmedi in the area, while the former also fired wide when well placed in front of goal.
(Reporting by Tim Hanlon in Barcelona; Editing by Rex Gowar)
