The Reds winger suffered a sprained left ankle (the same one he seriously injured last season) and was forced off at half-time in a match that ended 0-0 despite featuring plenty of goalmouth action.
Ecuador manager Reinaldo Rueda felt his players had come in for some rough treatment and called for greater protection from referees.
"The referees must take care of this situation because it [the injury] happened in the first half and [Antonio] was no longer the same," Rueda said. "He could not stand or walk on it and we had to make a change.
“It's a shame because we all know the process he went through to be here.”
Valencia, who missed almost six months of the 2010/11 campaign with an ankle injury sustained in September, is now a doubt for Ecuador’s next Copa America fixture, against Venezuela on Saturday 9 July.