The visitors reclaimed the Calcutta Cup following a hard-fought victory in terrible conditions, with sub prop Ellis Genge claiming the only try of the game.
But Jones was unimpressed by the Scotland fans in the capacity 67,000 crowd.
"It was an old fashioned Calcutta Cup game, swirling wind and an aggressive crowd without manners," said Jones in his post-match interview on BBC television.
"I thought you were supposed to show respect."
It is thought Jones was referring to the booing of England stand-off Owen Farrell as he was kicking for goal.
Former Scotland captain and BBC pundit Andy Nicol would like to see an end to the jeering of visiting kickers.
"It's something we need to eradicate," he said.