United had appeared to be strolling through the match, thanks to Danny Welbeck demonstrating lethal finishing with two goals in just 80 seconds to justify his place at the expense of Dimitar Berbatov.
But United had been given ample warning about Basle's threat with the Swiss side missing a hatful of chances before they stunned Old Trafford with three goals, two from Alex Frei and one from his namesake Fabian Frei, before Young's last-minute header saved a point for United.
Basle remain on top of Group C in the Champions League and this performance will provide Ferguson with some head-scratching, with question marks particularly against Phil Jones and Rio Ferdinand's compatibility in central defence.
The first half was all about Welbeck, however - having been a loan striker last season, the 20-year-old was a lone one against Basle with Ferguson surprising everyone, and not least Berbatov, with his formation.
Ryan Giggs played a key supporting role to Welbeck and was devastatingly influential with the vital touches to allow the young striker to finish.
The first came from a well-worked move. Jones brought the ball forward, Antonia Valencia took over and picked out Fabio's run into the box. A simple ball across the box was cushioned by Giggs into Welbeck's path and although he scuffed his shot slightly it still found the corner.
Just over a minute later and Giggs played a masterful ball that Welbeck struck home with a powerful low shot to make it 2-0.
Basle must have been cursing themselves with both Freis and Marco Streller all having missed the target from decent positions.
Basle coach Thorsten Fink must have been tearing his luscious blond air out, but the second half was a different story.
David de Gea had saved with his foot from Streller before Fabian Frei put the visitors back in the game. Streller headed on a corner and when the ball reached Frei 12 yards out he cracked in a blissful volley off the upright.
Fabian Frei then turned provider, crossing for Alex Frei to leave de Gea grasping thin air as the header soared into the net to equalise.
Ferguson had to go for it and he threw on Nani for Fabio with Valencia dropping to right-back.
Nani's first contribution was a negative one, however, as he gave the ball away and Basle surged forward. United's failure to clear their lines cost them dear as Streller burst into the box and Valencia brought him down.
Alex Frei made no mistake from the spot, blasting it high past De Gea and Old Trafford was stunned into silence.
Ferguson sent on Berbatov with nine minutes left and the Bulgarian had one chance with a header but Yann Sommer made a comfortable save.
The expected siege of Basle's goal arrived as time ticked away and finally Nani's cross found Young at the far-post and he headed it powerfully past Sommer.
Welbeck could have made himself the hero of the night in injury time but glanced his header just wide - and a winner for United would have been barely deserved.