Celtic go into their final group game against Spartak Moscow on Wednesday level on points with Benfica in the battle for second place.
Benfica make the daunting trip to Barcelona, who have already sealed their progress, but Messi hopes to help out Celtic after being impressed by their fans.
The style of football played by Neil Lennon's side has previously been criticised by Barcelona, but the Hoops pulled off a superb victory over the Spanish giants at home last month after an agonising late defeat at Camp Nou.
"The Celtic fans deserve to be in Europe," Messi told the Daily Record. "They have been amazing in both games we have played against them recently.
"We knew what they were going to be like in Glasgow, but the way they were in Barcelona after they had just lost in the way they did was amazing.
"I have never seen anything like that before.
"We have not always been supportive of the way that Celtic try and play football. However, their fans deserve the knockout stages of the Champions League as I think the competition would be a quieter place without them."