Jones's goalkeeper, Chris Kirkland, appeared to be punched by a Leeds fan who entered the field in the wake of Michael Tonge's 77th-minute equaliser, while unsavoury chanting also marred the night.
A large number of the Leeds fans housed in the Leppings Lane End sang about the child abuse charged which were dropped against Jones in, while former broadcaster Sir Jimmy Savile, now the subject of a similar police investigation, seemed to be heralded in song.
The Wednesday fans also stoked things up with songs about the two Leeds fans killed in Turkey in April 2000, with the Leeds supporters responding by throwing bottles onto the field and clashing with police.
"They are vile animals," Jones said. "You talk about racism, the chanting, that's a form of racism. And then (for the Leeds players) to go and wave at them... not in my book. You don't wave at them after that.
"I thought it had gone out of our game. The authorities have to look at it and sort it. I'm talking about an incident when we should be talking about the football. We're talking about vile animals. That's what they are. We talk about racism, but that, we need to sort that."
Leeds issued a statement after the game pledging to hunt down the man involved in the Kirkland incident. It read: "Leeds United Football Club would like to publicly apologise and condemn the action of the fan who came on the pitch and attacked Sheffield Wednesday goalkeeper Chris Kirkland. The club will fully co-operate with the police and the football authorities in identifying the individual concerned."
Jones went on to criticise opposite number Warnock for allowing his players to clap the fans at the end of a game which finished 1-1, adding: "We talk about morals and they go and wave at them..."
Meanwhile, Warnock called for Kirkland's assailant to be given a prison sentence as he described the events at Hillsborough as "an absolute disgrace".
Warnock told Sky Sports 1: "Dave (Jones, Wednesday manager) was saying we shouldn't thank the crowd but our crowd were fantastic but we've got one moron and I can't tolerate that."
South Yorkshire Police have pledged to work with both clubs to find the supporter who invaded the pitch and assaulted Kirkland.
And, in a statement, South Yorkshire Police's chief superintendent Jason Harwin said: "During tonight's match, Sheffield Wednesday versus Leeds United, at Hillsborough incidents occurred where it is believed seats and bottles were thrown inside the ground.
"We are also aware of an incident whereby the Sheffield Wednesday goalkeeper has been assaulted by an individual who ran onto the pitch. Fans are still leaving the ground and surrounding areas and our priority is to ensure the safe departure of fans.
"Such incidents are not acceptable and won't be tolerated. We will be working with both clubs to identify and quickly bring to justice the persons responsible. Thankfully, such incidents are a rarity and we see a minority spoil it for the majority of genuine supporters."