The 46-year-old feels the Ecuadorian should have received the same treatment as Bastian Schweinsteiger and insists Tuesday's match was always going to be tough.
Bayern Munich sporting director Matthias Sammer feels Manchester United's Antonio Valencia should have been sent off in the first-leg of their Champions League quarter-final at Old Trafford.
Already on a booking, the Ecuadorian winger threw himself into a challenge with Jerome Boateng during Bayern's 1-1 draw with Manchester United on Tuesday night.
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He escaped punishment from referee Carlos Velasco, although the official later sent off Bayern goalscorer Bastian Schweinsteiger after the midfielder picked up a second caution for a foul on Wayne Rooney.
"If you apply the same standards then I don't know how Valencia stays on," Sammer told Sky. "If the referee has a policy, then he must go through with it.
"There's no question that what Schweinsteiger did was a foul, but with Valencia, there were also several fouls, including his outstretched leg against Jerome Boateng. At this level, you have to apply the same standards."
Many thought Bayern would brush aside a faltering United in the first leg at Old Trafford on Tuesday, but David Moyes' men held their own to remain in with a chance heading to Munich next week.
Despite the two sides' differing fortunes so far this season - Bayern have already retained their Bundesliga title, while United sit seventh in the Premier League - Sammer insists he knew the tie would be no straightforward task.
"We sounded a warning ahead of the game in Manchester but people turn a deaf ear at times," he added. "They played just as we expected. They were very strong physically, organised and they tried to play on the counter.
"They managed that really well and they made life difficult for us. But that’s what you expect in the Champions League - it's the top level of the game. So we accept it and we’re happy with the result."