Messi scored a brace after Luis Suarez's opener as Barca took control of their Champions League semi-final by winning the first leg 3-0 at Camp Nou on Wednesday.
The forward's second was a tremendous 30-yard free-kick which brought up his 600th goal for the La Liga giants.
Valverde said he was unsure how Messi continually delivered for Barcelona and the 31-year-old is still surprising the head coach.
"I just saw it [the free-kick] at pitch level, but the truth is, Leo's always surprising," he told a news conference.
"It was very far out, we didn't know what he was going to do. In the end, I don't know how he does it, but he always does.
"I'd rather not think how he does it, to be honest, but he always shows up when we need him the most, this time just when we were in situations in which we had to shake Liverpool's domination off.
"Through the way he plays and the way he gets close to their goal, he helped us play and win by a bigger margin – and he instills fear into our opponents."
Suárez— FC Barcelona (@FCBarcelona) May 2, 2019
"THAT guy's goooood." pic.twitter.com/6ugGrpLm2O
Messi has scored 48 goals in 46 games this season for Barca, who have already won La Liga and would complete a treble with the Champions League and Copa del Rey.
The Argentine has also netted 26 times against English clubs in the Champions League, the most by any player against a single country’s teams in the competition, though Cristiano Ronaldo is level with him having hit 26 times against German opposition.
Messi became Barcelona’s all-time leading scorer with a hat-trick against Granada in 2012, moving him ahead of Cesar Rodriguez who last scored for the club in 1954.
He now sits 368 goals clear of Rodriguez, who is still the club’s second-leading scorer, while team-mate Luis Suarez sits fifth on the club’s all-time list with 177 strikes to his name.