Derek Young’s strike brought the Dons level but in the dying seconds, it seemed substitute DaMarcus Beasley had won the game for the visitors.
He steered the ball home as the match moved into injury time but was wrongly flagged offside and the goal was disallowed.
Kris Boyd had been beyond the final man but wasn’t interfering with play and the American’s effort should have stood.
Referee Craig Thomson’s decision means Gers’ 100% record has now come to an end ahead of the Old Firm clash with Celtic at Parkhead next week.
With Scottish referees under intense pressure to get major calls right, this result further brings their role into the limelight.
Smith made three changes to the side that beat Hearts, with Steven Davis coming in to make his second debut for the club.
Kenny Miller also made his first start for the club in the SPL, while Nacho Novo was deployed in attack beside Boyd.
Among the substitutes was Spanish youngster Aaron, one of the three under-21 players required in the matchday squad.
Rangers took the game to their opponents in the early stages, with Nacho Novo finding room in the box to turn and curl just over the bar from 15 yards.
Pedro Mendes also came close, drilling across goal and wide with his right foot after the home defence failed to clear.
Aberdeen offered little in return, with a tame Charlie Mulgrew free kick sailing straight into Allan McGregor’s arms.
For all the possession they were enjoying, it took the Light Blues time to press home their superiority.
But they eventually did just that midway through the first half when stand-in captain Weir nodded them in front.
Novo was fouled on the right wing and when Kevin Thomson swung the free kick in, the skipper rose highest to head in from close range beyond Jamie Langfield.
Going in front allowed Gers to stretch the Dons and that almost led to a second from Spanish striker Novo.
Davis played him in behind the home defence and having got past Scott Severin, he lobbed over Langfield too but the ball flew across goal and wide.
Novo was in again when Kris Boyd split the back line but a combination of Langfield and Severin stopped him from pulling the trigger.
Boyd had a chance himself moments before the break but his effort on the turn from a Davis pass was always fizzing past the post.
And Rangers paid for failing to take their chances when the Dons drew level on the stroke of half-time through Young.
McGregor seemed to have done enough when he saved well at point-blank range from Lee Miller after Mulgrew’s cross.
But the rebound fell to Young and his rising shot soared in to give Jimmy Calderwood’s men a share of the spoils at the midway point.
Gers tried to turn the screw after the break and continued to have more of the ball than their opponents.
Novo had an opportunity when he was played in on goal but was off target and after winning a corner, Mendes just missed out when he connected with Davis’ cross.
Of all people, it was Sasa Papac who almost put Rangers back in front when Boyd knocked down to him three yards out.
But Langfield beat the Bosnian to the ball and scrambled it clear, leaving the match delicately poised as it lurched into the closing stages.
Smith put Jean-Claude Darcheville on for Novo with 17 minutes left in a bid to secure all three points.
But Bougherra almost gifted them to Aberdeen when he was short with a passback and McGregor did well to smother the ball when Darren Mackie tried to capitalise.
Beasley was also thrown on for Miller although with time running out, it seemed the switch might be coming too late.
That appeared to change when the former PSV Eindhoven star beat Langfield with seconds remaining – but Thomson chopped his effort off and it stayed 1-1.