Officers were called to a convenience store in the 400-block of Kenderdine Road at roughly 4:45 a.m. on May 12.
An employee reported two masked men had entered the business carrying an axe before stealing packages of cigarettes. The suspects then fled the scene.
A suspect vehicle was stopped nearby, police said, and inside they located cigarettes, masks, and an axe.
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The two Saskatoon men were taken into custody.
They are facing charges that include robbery.