After a bright start from England in which Harry Kane had two good chances to add to his England tally, the drama flared at the other end.
Luke Shaw, who had been a great threat going forward, kicked high to clear the ball at the back and caught Loic Nego in the head as he moved to beat the England man to the ball. Spanish referee, Alejandro Hernandez, pointed to the spot and VAR saw nothing to correct his decision.
Roland Sallai sent Jordan Pickford the wrong way and finished confidently to given the hosts their first real challenge of this international break.
England upped the ante going forward after falling behind but were met with persistent fouls by their visitors. A third in quick succession, on Jack Grealish down the right, and England punished Hungary.
Phil Foden whipped a cross in low and saw it deflect off a red shirt to the far post where Stones bundled home for his first England goal since scoring two against Panama at the World Cup in Russia.
England pushed for a winner for the rest of the night but never looked dangerous enough going forward.
Here is how Jack Rosser rated the Three Lions…
Not overly at fault over the penalty and had little to do other than that.
Tireless in his running to get forward and untroubled defensively.
Untroubled at the back and showed good awareness to get to the back post and score his goal.
Solid enough showing at the back though largely untested. Nothing much in his performance to worry Harry Maguire.
Can feel hard done by over the penalty decision. Looked to get forward wherever possible and was one of England’s more threatening players.
Kept things tidy and ticking over in midfield.
Tried to be positive on the ball but struggled to break the lines going forward.
Didn’t hit the heights of his showing in Andorra but delivered the cross which produced Stones’s goal.
Extremely wasteful on the ball and didn’t link well with others around him.
Won the free-kick which brought about England’s equaliser but struggled to make things happen thereafter.
His club form has now reached England. The first time Kane has not scored in a qualifier since September 2017.
Made a couple of good runs down the wing with the ball but then dropped to wing-back by Southgate.