As a result, PSV will need to win this one to have any chance of accomplishing that, but even a win here could see them out of the running if Tottenham beats Inter.
PSV manager and former Barcelona midfielder Mark Van Bommel could not disguise his disappointment at an opportunity lost for the Dutch champions, who will finish bottom of the group.
Messi's goal broke the scoring drought by both sides, giving Barcelona a 1-0 lead by working through a tight space and multiple PSV players before lacing home the opener. With Suarez out, Ousame Dembele will likely move into the starting XI.
Both Sergio Busquets and Ivan Rakitic were guilty of some very bad passes early on that could have got the Catalans into trouble.
De Jong headed against the bar just before half-time and Denzel Dumfries struck the post on the rebound.
'We gave everything, had a good idea, a good way of playing and created so many opportunities.
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Harry Winks hit the frame of the goal as Spurs pushed for the win they needed and substitute Christian Eriksen duly provided it 10 minutes from time when he fired home from close range.
Picking the ball up in midfield, Messi drove forward and found Dembele, before running beyond the Frenchman, who slipped the ball back to him.
De Jong eventually got the goal which he and PSV deserved but Barcelona held on and will be in the last 16 yet again, as group winners for the 12th season running.
Zoet had to keep out a powerful Messi strike early in the second period as Barcelona started on the front foot.
Barca were thankful to Messi for stirring them after a below-par hour of play in which they could have been punished by the hosts.