Messi appeared to be suffering from soreness in his groin early in the second half as Barca ran out 1-0 winners in Saturday's La Liga clash at the Santiago Bernabeu.
The Barca captain was also involved in a first-half flashpoint with Madrid counterpart Sergio Ramos, who later denied deliberately pushing his arm into the forward's face .
Messi was clearly unhappy with the referee's decision not to punish Ramos over the incident, but his side won at the home of their rivals for the second time this week as Ivan Rakitic's goal moved Barca 10 points clear at the top of La Liga.
Ramos used a post-match interview to all but concede Madrid's title dreams are over, with Santiago Solari's men now 12 points off the pace and Barca on track for the treble.
An injury to Messi would have dented Barca's hopes of success on all fronts, but with a Champions League last-16 second leg against Lyon to come, Valverde shrugged off suggestions Messi was hurt as Barca made history by becoming the first team to win three straight away games against Madrid.
"Messi is fine," said the Barca boss. "He has had a great game and made a great effort.
"He is an extraterrestrial in a way, because every time he takes the ball something extraordinary happens."
And although Madrid's hopes of unseating the defending champions look to be over, Valverde is taking nothing for granted in the title race.
"There is a world ahead," added Valverde. "Real Madrid are capable of winning many matches in a row, but there is also Atletico.
"We respect our opponents just as they respect us and it is absurd to start thinking about the league when there are so many games left.
"Last year we had more distance in the league and they were European champions, they are a candidate to make history in any capacity.
"We have been much better than the other day [Barca's 3-0 win in the second leg of the Copa del Rey semi-final], we wanted to have control but the ball did not flow too much.
"We had a good attitude, today we took a step forward and when we dominated we hurt them."