The two teams ended up drawing the game 2-2, with Hector Moreno nodding a late equaliser, and there was controversy when Nani's 21st-minute effort was disallowed for offside - with the use of VAR - before Ricardo Quaresma's opener.
While the VAR appeared to come to the correct decision, Santos was frustrated that this came only after the officials had looked at an earlier phase of play where Pepe was offside.
"Those are the rules and if [the VAR] benefits football, very well," he said. "No one has understood it very well yet.
"It was in the previous move after Cristiano [Ronaldo]'s shot hit the crossbar. It's very confusing.
"There was a stoppage for [Cedric Soares'] other goal, too. It is always our goals. Let's accept it."
Despite the disappointing end with Moreno's goal, Santos believes a draw was a fair result.
"We played a team that has very good, technical players," he said. "At the beginning we couldn't enjoy good control of the ball, but then we managed to balance things out and could have won it in the end.
"The result was fair as Mexico also played well."