The 30-year-old had expected to be on the pitch and was even confirmed fit the previous day in the pre-match press conference by Argentina boss Jorge Sampaoli, but after feeling discomfort in his hamstring and adductor the night before the game, he and the coaching staff decided it was not worth the risk.
It was that same problem that kept the five-time Ballon d'Or winner out of the 2-0 win over Italy in Manchester four days earlier. But instead of returning to his club, Messi was keen to stay with the group in their preparations for the World Cup — and he was eager to start against Spain in Madrid.
Argentina equal worst ever defeat with horror show in Spain
As far as final tune-ups before World Cup team selection goes, Argentina's showing on Tuesday was about as bad as it gets.
With Lionel Messi still sidelined, the Albiceleste were put to the sword by Spain, with Isco's hat trick leading La Roja to a dominant 6-1 victory.
The defeat was the joint-largest for Argentina in their history, with the South American side also having suffered 6-1 losses at the hands of Czechoslovakia at the 1958 World Cup and Bolivia during qualifying for the 2010 World Cup.