Valencia was on a booking when he went into a full-bloodied challenge with Jerome Boateng in the second half, but escaped punishment from Spanish referee Carlos Velasco Carballo.
Bayern goalscorer Bastian Schweinsteiger did see red, though, picking up a second booking for a late foul on Wayne Rooney to rule him out of the second leg in Germany.
Sammer said on Sky in Germany: "If you apply the same standards then I don't know how Valencia stays on. If the referee has a policy, then he must go through with it.
"There's no question that what Schweini did was a foul, but with Valencia there were also several fouls and his outstretched leg against Jerome Boateng. At this level you have to apply the same standards."
The away goal means Bayern are still clear favourites to reach the semi-finals and club chairman Karl-Heinz Rummenigge said the result was a "great" one for the visitors.
Speaking at the club's traditional post-match banquet, he was reported by DPA as saying: "If you want me to put it together in one sentence, I would say: not won, but still very happy. I believe the 1-1 is a great result."
Midfielder Toni Kroos was also not displeased with the draw, even though holders Bayern had been clear favourites to win ahead of the game.
He told the club website: "It was a tough game. We dominated the match, but Man United gave their all and they were dangerous.
"We deserved the 1-1 draw at the end of the day.
"The result's okay. We've got every chance in the return game."
The Germany international has been linked with a move to Old Trafford given the uncertainty over his future at the Allianz Arena after so far failing to agree a new contract.
He added in Munich's TZ newspaper: "It (Old Trafford) is a beautiful stadium. But I belong to Bayern Munich and that's good."
Rummenigge added: "He will certainly play at Bayern next year. What's beyond that, I don't know."