"Eduardo didn't fall theatrically," Markovic told Reuters. "There was some contact at first and he fell afterwards.
"Eduardo has such a light (physical) constitution that a strong gust of wind could knock him over. But Eduardo is not the type of man or player who would simulate."
UEFA opened a disciplinary case against Eduardo after the Brazilian-born Croatian went down in the area under challenge from the goalkeeper and won a penalty in Arsenal's Champions League play-off against Celtic.
Croatia are preparing for World Cup qualifiers at home to Belarus and away to England and the influential Luka Modric will miss both games after he suffered a fractured fibula playing for Tottenham Hotspur against Birmingham City on Saturday.
"There is no doubt that we are very much handicapped because Luka is our main playmaker and his absence will also be felt in the English league," Markovic said.
"But soccer is a game where all kinds of things happen and there is no doubt that it was a duel like any other.
"It is neither the first nor the last time in soccer that main players are absent for major games."
Croatia are in second place in World Cup qualifying Group Six and trail England by seven points.
Modric suffered the injury, which will sideline him for around six weeks, against the same team that caused Eduardo such grief in February 2008.
Eduardo suffered a horrific multiple fracture which threatened his career and sidelined him for a whole year.
