Aleer's move to the Saints appeared a formality for weeks after he requested a trade following the Giants' elimination final exit.
But St Kilda, who have embarked on an expensive recruiting period, decided to ditch their long pursuit of the 24-year-old.
The move has blindsided Aleer and his manager Dylan Smith, as well as the Giants, who have committed to bringing in experienced Essendon defender Jayden Laverde.
"Leek is shattered. He's incredibly disappointed," Giants football boss Jason McCartney told Trade Radio about Aleer's reaction to St Kilda abandoning their interest in him.
"He loves our footy club and was in tears at the exit interview.
"There's a contract there with us ... he's more than welcome to be playing at the Giants."
North Melbourne's football talent boss Brady Rawlings confirmed the Kangaroos have discussed Aleer's situation.
After finishing in the bottom-three for a sixth-straight season, North are desperate to add key position talent to a squad stacked with gun midfielders.
"We have been in touch with Leek's manager," Rawlings told Trade Radio.
"He is pretty disappointed.
"We have discussed it as a club, we are still doing the work on it."
But Rawlings also said North would "back our guys in" when asked about filling defensive positions.
A number of clubs, including reigning premiers the Brisbane Lions, have already ruled out making a play for Aleer.
St Kilda, who have received criticism from managers and rival clubs, are yet to publicly respond to pulling their offer with just five days remaining in the trade period.
The Saints signed Carlton pair Tom De Koning and Jack Silvagni as free agents, while trading for Gold Coast midfielder Sam Flanders and West Coast premiership player Liam Ryan.
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