In the second minute the England midfielder's free-kick sailed straight into the Stoke goal but referee Andre Marriner - with a linesman's flag raised - ruled out the effort.
Television replays showed Dirk Kuyt, who followed the ball into the net, was not in an offside position.
Stoke then mounted a magnificent rearguard action to claw their way to a 0-0 draw.
"The disallowed goal was a key decision. If that had been allowed it would have been much more open game," said Benitez.
"I have no idea why the goal was disallowed. The referee told Jamie Carragher that it had been his decision, not the linesman's.
"But it was a massive mistake. And nobody knows why the effort was ruled out."
Gerrard, who had taken his goals tally for the club to 99 with a double in Marseille in midweek, was engulfed by celebrating colleagues before Liverpool realised the effort had been ruled out.
Benitez said: "The players worked very hard. They tried everything, but maybe we needed a little more ability in the last third to make use of all that possession and all those shots."