Raphael Guerreiro headed in Ricardo Quaresma's cross in second-half stoppage time as Portugal sealed a third consecutive 1-0 triumph.
All the talk in the build up to the friendly at Old Trafford had been of the clash between Lionel Messi and Cristiano Ronaldo, but both men were substituted at half-time having had a minimal impact on the game.
Messi struck the post in the 11th minute as Argentina made a bright start, but Santos was pleased at his team's response after coming under pressure during the early stages.
"The first 20 minutes our team were very, very bad," the Portugal coach told RTP.
"We allowed Argentina to play and we were always late to the ball.
"It is worth nothing the delivery, availability and capacity of players to run, but we have the capacity to do more.
"The game grew more balanced. Portugal started to have more of the ball. In the second half I made some changes, there were some tired players.
"We defended better but always had difficulty getting out to attack. In the last 10-15 minutes the opponent dropped a bit and we ended up making the goal.
"The team did not concede a goal in the last three games and that's very important."
