Argentine referee Nestor Pitana disallowed a goal by Portugals Pepe in the 21st minute of the first half after consulting the video assistant referee.
Mexico's all-time leading goal scorer Javier Hernandez pulled one back for his side with a classic flying-header in the 42nd minute with both teams going into the break 1-1.
With time running out, Southampton right-back Cedric pounced on a loose ball and slammed home Portugal's second goal.
Mexico claimed a 2-2 draw with Portugal in their Confederations Cup opener on Sunday with a last-gasp equaliser by Hector Moreno.
CRISTIANO RONALDO failed to appear for the usual post-match interview after being named man-of-the-match for Portugal in their 2-2 draw with Mexico.
Portugal play hosts Russian Federation in Moscow on Wednesday, while Mexico take on New Zealand in Sochi.
Portugal ended 2-2 with Mexico and, perhaps fortunately for FIFA, Chile beat Cameroon 2-0. Find us on Facebook too!
Portugal celebrated, but the game was then held up as the referee waited for the assistant to check the replay, before the goal was ruled out roughly 40 seconds later because Pepe had been adjudged to be offside.
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"It wasn't the result that we wanted", he said.
Portugal had the ball in the net shortly before the midway point in the net as Cristiano Ronaldo saw his volley acrobatically turned onto the crossbar by Mexico goalkeeper Guillermo Ochoa.
'The team continue to believe in qualification, we have great possibilities, because there are still two games left'.
Cedric Soares looked to have given the European champions the three points with a goal in the 86th, but newly-signed AS Roma defender Hector Moreno scored off a corner to rescue a point for the CONCACAF representatives.
Quaresma could have doubled his tally just before halftime after a Ronaldo backheel gave him an opening, but the ball got stuck under his feet and could only drag his shot just wide, when the opportunity had promised so much more - and Portugal were made to pay.
"Now we have to think about the next match because we must win".
"If we have a free afternoon perhaps one or two of us will go over there", Germany midfielder Joshua Kimmich said.
The veteran forward was one of the standout performers in Portugal's Euro 2016 triumph a year ago, and he seems to have continued his form for the Seleccao in the Confederations Cup as well.
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