"What Cristiano and Juventus did on Tuesday was impressive," Messi said reporters. "It was a big surprise. I thought Atletico would be a lot stronger, but Juve were all over them and Cristiano had a magical night," he added.
Meanwhile, Messi scored twice and adding two assists on Wednesday as Barcelona hammered Lyon 5-1 after drawing the first leg 0-0 in France last month.
Messi's Barca could potentially face Ronaldo's Juve in the last eight if the two sides are paired together in Friday's draw for the next round.
"We don't want to choose one [side] because they're all really tough," Messi said. "[Manchester] City, Juventus, Ajax, who have a great team of kids and don't fear anything, Liverpool, who've shown they pack a punch...
"We're relaxed and what we have to prepare for is the toughest test possible, which is what's coming now in the final stage of the season."
Messi opened the scoring against Lyon from the penalty spot before Philippe Coutinho doubled the home side's lead at Camp Nou before the break.
Ronaldo had hit a hat trick as Juve to beat Atletico 3-2 on aggregate and book their place in the last eight.