The Tottenham star did not reappear after half-time following a lower-back injury as Chris Coleman's men fought back from a goal down to claim a deserved win at Hampden Park
Two goals within the space of a minute, a penalty from Aaron Ramsey and a Hal Robson-Kanu header helped Wales claim a 2-1 win away to Scotland.
The home side had gone into the half-time break ahead after Grant Hanley’s added-time header, but were reduced to 10 men when Robert Snodgrass saw red for a foul on Chris Gunter that led to the away side’s equaliser.
And one minute later Wales took the lead, but saw Ramsey dismissed for a needless foul on James McArthur seconds before the final whistle.
In his first competitive game in charge of the national team, Gordon Strachan handed a starting berth Hanley, alongside skipper Gary Caldwell in defence, while Charlie Adam was forced to settle for a place on the bench.
The visitors were boosted by the availability of Tottenham star Gareth Bale, who had been doubtful for most of the week after picking up an injury and being struck down with a virus.
And Scotland were handed a huge blow within the first minute, as Steven Fletcher rose for a header with Ben Davies, which saw the Sunderland striker taken from the field in a stretcher and experienced frontman Kenny Miller replacing him.
Wales dominated the opening stages, with the tormentor-in-chief Bale seemingly gliding through the Scotland defence at will, but they struggled to find the final ball to get in on Allan McGregor’s goal and open the scoring.
Miller was on the end of the first chance for the hosts’ midway through the first half, as he got onto the end of a cross from the right by Chris Burke, but the striker could only direct his header over the bar.
And just before the half-time whistle the unthinkable happened, as Scotland took the lead. Hanley, twisted and turned inside the area to beat Sam Ricketts to the ball and send a powerful header beyond Boaz Myhill.
Wales were handed another blow after the interval as Bale failed to reappear after suffering a lower-back problem, and was replaced by Jonathan Williams, with the visitors chasing the game.
But Wales were again the team controlling proceedings, only to be thwarted at the last but some stout Scotland defending before Robert Snodgrass rattled Myhill’s left-hand post with a curling effort.
The visitors finally made the breakthrough with 20 minutes remaining as Ramsey smashed home a penalty via the crossbar, before substitute Andy King found space down the right wing to feed Robson-Kanu less than 60 seconds later.
Scotland spent the closing stages desperately searching for a way back in the tie, and now face a daunting trip to Serbia on Tuesday while Wales welcome Croatia.