The Argentine experienced the Frenchman's quality in the round of 16 in Europe this season with Benzema scoring a hat-trick in the second half to knock PSG out.
Benzema bagged another four goals against Chelsea in the following round before scoring three in a dramatic win over Manchester City in the semi-finals.
The 34-year-old won the Champions League this season with Real Madrid as they overcame Liverpool 1-0. Benzema - who also lifted La Liga - was the top goalscorer in Europe and domestically this year with a total of 44 goals from 46 games.
"Out of the blue they score against you, and the match changes automatically," Messi added when asked about Carlo Ancelotti's side. "Madrid was not the best team in this Champions League, there were better teams."
Messi is currently with Argentina's national side in Bilbao ahead of the Finalissima - a fixture which sees the Copa America winners take on European Champions Italy.
While Argentina are a front-runner to win this year's World Cup in November, Messi insists it is the current holders who remain 'favourites'.
"France is an impressive team, (four years) ago we said they could be candidates and they ended as winners. I believe the hit they took at the Euros (being eliminated by Switzerland) made them stronger," Messi said.
"(Argentina) can fight anyone and will make it hard for any rival. That doesn't mean we are the favourites to be world champions or any of that. It means we will fight against anyone."