Appearing on BBC Sportsound, the ex-Scotland had his say on the SNP leader following the fallout from Rangers’ title celebrations.
He said: I don’t want to get involved in this political situation, I just hope she resigns. That’s all.”
It led host Kenny Macintyre to clarify that it was Levein’s opinion.
Stewart, a keen advocate for Independence, responded to the claim on Twitter.
He posted: “This will be the man who only last week said League 1 & 2 shouldn’t return this season because nobody thinks about the players, turned out PFA Scotland had done a survey with the players and roughly 95% wanted to return!
“This man has his finger on the pulse.”
Levein signed Stewart for Hearts in 2004 but the relationship has soured with the BBC pundit often critical of his former boss during his second stint as manager at Tynecastle.