Chile's star player Arturo Vidal fiercely argued with referee Damir Skomina when a goal scored in first-half stoppage time by Eduardo Vargas was overruled nearly one minute later.
More confusion was caused when Argentine referee Nestor Pitana called a review for unclear reasons after defender Cedric Soares's deflected shot in the 86th gave Portugal a 2-1 lead.
As it stands, Russian Federation sits at the top of the group, followed by Portugal and Mexico while New Zealand, who were thumped by the hosts 2-0 on Saturday, are bottom.
It had seemed as though Cedric had handed all three points to the European champions when he fired Portugal in front in the 85th minute but Mexico and Moreno had other ideas. Portugal has many good players along with Ronaldo.
"We played a team that has very good, technical players", said Portugsl coach Fernando Santos.
Osorio fielded a starting team entirely made up of players based in Europe and Mexico flew out of the blocks.
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After a 21st minute free kick taken by Cristiano Ronaldo struck the wall, the ball was sent back into the area where four Portugal players were in offside positions and one of them challenged for the ball, meaning he was offside.
Mexico had to come back twice against Ronaldo and co. and a result like this will surely strengthen Osorio's belief that his team has learned many lessons since a year ago.
Ronaldo obliged after Carlos Salcedo made an error to allow him in on goal before finding Quaresma in acres of space who collected the ball calmly before waltzing past Guillermo Ochoa to score the opener.
"We also managed to keep Cristiano Ronaldo in check".
Instead, he was too busy receiving treatment and issued only a brief statement on the result and Portugal's tournament hopes, avoiding any questions about his future for now.
'We have to win, because if we win the next game we will be one step away from qualifying'. They scored in the last few minutes and now we think of the next game.
The quality of El Tri's players would also have been debated.
Portugal's advance in the early stages was soon rewarded by Pepe latching onto a long distance effort from winger Nani, only to be retrospectively ruled offside.