Leeds United and South Yorkshire Police will work together to attempt to identify those responsible for the trouble in Friday night's game at Hillsborough as Sheffield Wednesday goalkeeper Chris Kirkland was attacked by a fan.
Wednesday and Leeds played out a 1-1 draw, but the result of the Yorkshire derby was overshadowed as Owls keeper Chris Kirkland was attacked by a fan. Leeds had just levelled through Michael Tonge when a fan came on to the pitch and shoved the keeper in the face.
As Kirkland lay prone on the ground, the fan dashed back into the crowd to make his escape. Support staff were quickly on hand to attend to Kirkland, who was treated for some time before playing on, although he was visibly shaken.
It is believed the fan responsible is based in Cheltenham and Gloucestershire Police has also confirmed its involvement in the investigations.
A large number of the Leeds fans also sang about the criminal charges that were dropped against Wednesday manager Dave Jones, while the late broadcaster Sir Jimmy Savile, now the subject of a similar police investigation, seemed to be heralded in song.
The Wednesday fans also stoked things with songs about the two Leeds fans killed in Turkey in April 2000; the Leeds supporters responded by throwing bottles onto the field and clashing with police.
Jones said: "I thought that had gone out of the game. The authorities have got to look at it and sort it, otherwise they will keep doing it. We should be talking about the football, it was a great game with great intensity, but they are vile animals, that's what they are, all of them. I don't care if I get in trouble for it. We go on about racism in the game. That we need to sort and quickly as it is an absolute disgrace.
"It is upsetting that they are allowed to do it. They should be banned from every away ground now."
Jones was also angered that opposite number Neil Warnock had asked the Leeds players to applaud the away fans at the final whistle.
"I really am fuming that he sent his players to clap them,'' Jones said. "For what? Wrecking a stadium, beating up my goalkeeper? They (Leeds) need to clean their house and get it in order. And they should be banned from every away ground until they sort it out."
Warnock told Sky Sports after the match that he was disgusted with the attack on Kirkland. "I thought it was an absolute disgrace," he said. "I think they should get the guy and prosecute him and put him in prison. (Kirkland) went down like a ton of bricks but that doesn't make a difference. Nobody should be on the pitch doing that.
"I hope we can make an absolute issue of it. He spoiled everything for everyone. I've not enjoyed that when I see a moron like that. I am not proud of being Leeds manager when I see that. I don't mind the rivalry between us - there was a great atmosphere. To see things like that on the field of play, there is no place for it - I am absolutely embarrassed."
He suggested, though, that Jones had been "a little bit carried away" with some of his post-match remarks.
"Dave is disappointed with not winning the game," he said. "Dave says a lot, he's looking that he's lost two points. I've been with Dave before and you do get upset if you don't get the right result as a manager and you have to take it with a pinch of salt.
"You don't mention anything detrimental about your own side or fans and I can't blame him for that because of the run they're on."
In a statement after the match, Leeds had said: "The club will fully co-operate with the police and the football authorities in identifying the individual concerned."
Chief Superintendent Jason Harwin of South Yorkshire Police added: "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. 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."
The Football Association has also confirmed that it will investigate the events.
Information from the Press Association was used in this report