The striker was sent off in Villa's 2-1 defeat against Tottenham on Sunday after pushing Ryan Mason in the face.
Both clubs have also been charged with failing to control their players after the melee following Benteke's clash with Mason.
Lambert admitted Benteke deserved to be sent off, but claimed he was provoked by Mason pushing his head into the striker's and feels the three-game ban is harsh.
He said: "We asked the FA to look at it, it was dismissed
If Christian has to go you have to look at other things (Mason)
Three games is excessive.
"I've not really had a chat with him as there's so much going on.
"The FA have made up their minds and the two teams look like they are going to get hit.
"The reaction from the players was normal
Spurs were obviously involved in it as well, but it was a situation where the guy put his head in Christian's face.
"He will learn from it
I don't condone what he did but I can understand why he did it."
The 23-year-old is back in the Belgium squad, for a friendly against Iceland and their Euro 2016 qualifier against Wales, for the first time since rupturing his Achilles in April.
Benteke only returned for Villa last month and is yet to score but looked close to his best against Spurs, and Lambert hopes the international break will give his striker the chance to regain his fitness
The manager said: "That, for me, is the big thing as it will get him games
It's good he's picked and if there's any good to come out of it he will still get games."
Source : PA