On a day when relaxed Covid restrictions meant a capacity crowd of around 50,000, Israeli striker Eran Zahavi dampened down expectations after less than five minutes when he curled in a free-kick.
Midfielder John McGinn levelled in the 29th minute with a drive but Munas Dabbur restored Israel’s lead two minutes later.
Lyndon Dykes had a penalty saved by keeper Ofir Marciano just before the interval but the striker made up for a poor effort early in the second half with a VAR-awarded goal.
Deep into six added minutes of a breathless encounter, McTominay bundled in a McGinn corner and bedlam ensued.
Steve Clarke’s side remain in second place in Group F on 14 points behind runaway leaders Denmark ahead of a trip to the Faroe Islands on Tuesday where three points will be expected in the quest for a play-off spot.
Clarke admitted he prayed that referee Szymon Marciniak would use VAR to give Dykes his goal.
He said: “Initially, from the technical area, I am looking at it and thinking it was a foul because the referee chalked it off.
“I turned to my bench and they are telling me straight away that there is no contact, so I’m praying that the referee goes to look at it on the monitor because I had a feeling when he went to the monitor that we would get the goal.”