A stunning free-kick from Eran Zahavi silenced sold-out Hampden after just five minutes until John McGinn lifted the mood with a curling finish from the edge of the box.
That boost though was immediately wiped by Munas Dabbur’s scrambled goal moments later which gave the visitors the half-time lead.
Lyndon Dykes had a poor penalty saved just before the break, but did find the leveller after a little help from VAR in the second half.
Then with Scotland pressing for a vital winner it finally came in the 94th minute when Scott McTominay headed in and Scotland moved four points clear in second place.
Here's how the players rated…
Player ratings scale - 10: One of best performances you've seen. 9: Outstanding. 8: Very good. 7: Good. 6: Average. 5: Poor, 4: Very poor. 3: Terrible day at office. 2: Abysmal. 1: One of worst performances you've seen.
9. Billy Gilmour - 8
Midfield conductor had Scotland threatening with sharp passing and brave for penalty win and dictated the middle of the park. Booked. Photo: Ian MacNicol
10. Che Adams - 6
Had chances but largely blunted by visiting defence before being replaced by Christie. Photo: JUSTIN TALLIS
11. Lyndon Dykes - 7
Made up for poor saved penalty with all-action second half and goal. Perhaps should have had another with header. Photo: Sammy Turner - SNS Group
12. Steve Clarke
Stuck with shaky defence, picked up team from below-par first half and they rewarded him with a late win that saw him sprinting along the south stand with joy Photo: Craig Foy - SNS Group