The dramatic conclusion to their qualifier at Hampden Park, and three-point haul, means Scotland consolidated second place in Group F as they moved to 14 points, four ahead of third placed Israel, with three matches each still to play.
Denmark lead the group with a 100% record after six games.
"We know they're a difficult team, but in the second half we dominated them in my opinion on the pitch. We created a huge amount of chances," said goal hero McTominay.
"At half-time, we knew we had to wake up. They were more aggressive, more aware, more compact as a team in the first 45 [minutes]."
Israel's goalkeeper Ofir Marciano made a penalty save from Dykes and two key stops to keep alive his own team's World Cup hopes before McTominay rose high to win the game for the Scots.
Israel stunned the crowd at a wet Hampden as Zahavi stepped up off the turf after being fouled by Jack Hendry in the fifth minute and whipped the resultant free kick over the wall and beyond the reach of Scotland goalkeeper Craig Gordon.
A sustained period of pressure from the home side led to McGinn's equaliser in the 29th minute as he curled a shot into the top corner from the edge of the area after being set up by some smart passing between Kieran Tierney and captain Andy Robertson.
Parity, however, lasted all but two minutes as Israel struck from another free kick. The effort did appear to hit Dor Peretz on the arm before Dabbur tucked the ball away but, after a VAR check, the goal was allowed to stand.
Scotland should have been level before halftime, however, when Billy Gilmour had his feet taken out from under him by Bibras Natcho as he attempted a shot from the edge of the box and a spotkick was awarded.
However, Dykes' penalty was straight down the middle and easy for visiting goalie Marciano to save with his legs.
Dykes did make up for the miss in the 57th minute to make the score 2-2 but it was only awarded after the Polish referee Szymon Marciniak went to the VAR monitor and overruled his own decision to initially disallow the attempt.
Dykes had been penalised for a foot high challenge but replays showed he touched the ball before any contact with defender Ofri Arad, at the end of a perfect cross from Robertson.