The delays while the VAR examined replays were a further negative aspect - the shortest for Portugal's first disallowed goal was 56 seconds, while the longest - for Cedric's allowed goal - 2 minutes 9 seconds.
Real Madrid pair Cristiano Ronaldo and Pepe have been caught complaining during Portugal's draw with Mexico.
Mexico plays New Zealand in its second Confederations Cup game on Wednesday.
Another loss will nearly certainly end any semi-final hopes before facing European champions Portugal in their final pool match. Chile was also made to wait for a review before a goal was confirmed. "We had enough chances to win the game".
Portugal captain Cristiano Ronaldo: "It was not the result we wanted, the team had nearly won and we suffered in the last minutes, but this is football".
"We played a team that has very good, technical players", said Portugsl coach Fernando Santos. The setting only reinforces the sense Germany is taking a more casual approach to this eight-team tournament than the Australians. The match against Mexico and a subsequent 1-1 draw with the United States was valuable and rare preparation for New Zealand, which is used to playing teams below the level of CONCACAF's best or even mid-tier teams from our region.
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Ronaldo played well and made the first goal but did not score.
Borussia Dortmund midfielder Raphael Guerreiro failed to deal with a cross into the box and Carlos Vela teed up Hernandez, who met the cross with a diving header.
Cristiano Ronaldo's initial shot hit the crossbar then Pepe "scored" from the rebound in the 22nd minute. It was perfectly placed for Chicharito to get a head on the ball, and Mexico's all-time leading scorer converted.
The referee was advised the video assistants were examining the goal and they spotted the offside player.
But with the 90 minutes up, Mexican defender Moreno rose highest from the final corner of the game to head in the equaliser.
Mexican players a year ago launched their own campaign against homophobic slurs during matches.
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