England held as Hungary fans clash with police
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Gareth Southgate's side fell behind to Roland Sallai's penalty before Stones levelled late in the first half.
Despite dropping points for just the second time in their eight Group I matches, leaders England remain on course to qualify for the World Cup.
They are three points clear of second-placed Poland and will be sure of reaching next year's tournament in Qatar if they take four points from their final qualifiers against Albania and San Marino in November.
After the 5-0 rout of Andorra on Saturday, this was a more serious test against a Hungary team that acquited themselves well at Euro 2020 and Southgate will be concerned by England's erratic performance.
"Disappointing performance. Full credit to Hungary, they caused us a tactical problem and we were not fluid," Southgate said.
"We did not play at the level we need to, simple as that. We will look at the balance of the team.
"From the start, we were not sharp, gave the ball away and were over-running things. For the first time in a long time we have to hold our hands up."
The police had moved in to arrest one fan for a "racially aggravated public order offence" following comments made towards a steward.
As the scuffles became more vicious, police with batons were pushed back by the hooligans before order was finally restored.
The violence in the stands might have caused England to take their eye off the ball and they were punished in the 24th minute.
Luke Shaw raised a high boot as he tried to clear on the edge of his own penalty area, in the process catching Loic Nego in the head.
The challenge could have been viewed as accidental, but a VAR check confirmed the penalty, leaving England fuming as Sallai sent Jordan Pickford the wrong way with a clinical spot-kick.
- England frustrated -
Jack Grealish's quick feet drew a foul from Attila Szalai wide on the right flank.
Phil Foden whipped over an inswinging free-kick that flicked off Declan Rice before Stones bundled it into the net from close-range.
Southgate is aware that England's failure to create more chances cost them dearly when they failed to build on their lead in the Euro 2020 final defeat against Italy in July.
He had spoken this week about his desire to play with two creative central midfielders in preparation for the World Cup and, with that in mind, he started Foden and Mason Mount alongside the more defensive Declan Rice.
The experiment was hardly a resounding success as England lacked rhythm and tempo.
When Southgate replaced Grealish with Bukayo Saka in the second half, the Manchester City forward's head-shaking response suggested he was not pleased with the decision.
Raheem Sterling should have lifted the mood moments later when he sprinted onto Harry Kane's pass, but his finish was weak.
Kane has yet to score a Premier League goal for Tottenham this term and it was another subdued display from England's captain, who failed to score in a qualifier for the first time in 16 games.
There were few sights of goal for Kane, whose lack of touch was encapsulated by a shanked effort that flew well wide moments before he went off.
Winners of their previous 21 home major tournament qualifiers since a draw against Ukraine in 2012, England's spluttering display brought an end to that impressive streak.