"He's got this talent nobody else has", Valverde told reporters.
"There is not one player who doesn't think about defending at all, but you have to adapt to the qualities of your players".
With Barcelona leading 1-0, Messi provided a sublime cross in to Arturo Vidal as the Chilean double their lead.
Atletico Madrid may have performed with a drop of Messi's attacking inspiration as they have been held to a disappointing draw by Alaves.
The Argentine's incredible performances over the last 15 years make him one of the top three players in Barca's history, according to Guardiola.
Barcelona struggled without Messi but has won all of its matches since he returned as a starter following a right calf injury he picked up in the preseason. "He is from another planet".
The Barcelona captain went on to force a save from Matip minutes before the break and carried that intensity over to the second half.
Two moments of Messi magic restored order at the Camp Nou with the Argentine playing a ideal ball into the penalty area for Arturo Vidal to volley home and then curling in an unstoppable free kick shortly after to give Barcelona a 3-1 lead at half-time.
Messi brought down a pass while about 35 yards from the net before drawing three Valladolid defenders.
Messi missed out on a hat trick when his close-range shot in stoppage time went wide. We have in memory what we have done but we want to look forward and win this league.
The 32-year-old has missed Argentina's past four matches - all friendlies - but is in line to make his return in November after being named in Lionel Scaloni's latest 26-man squad.