The animals were pinched from Bruno's near Daventry late last month, police said.
Store manager Jackie Hunt told the Northampton Chronicle the thief removed the tortoises from a locked vivarium then put them in his pockets.
Police confirmed the thief "concealed" his booty "in his trousers" and appealed for witnesses.
More news from Northamptonshire
"We saw the CCTV later and it clearly showed the man bending down and breaking the lock, before taking out the tortoises," Mrs Hunt told the BBC.
"He was wearing jogging bottoms and he put one in each pocket."
The micro-chipped tortoises, worth about Â£150 each and about 7.5cm (3in) in length, are too young to survive without correct UVB lighting and heat.
Their micro-chips are registered on the tortoises' licences, which are still held by the pet shop, meaning they cannot legally be owned in this country.
The theft happened at the shop in Whilton Locks Garden Village at about 16:00 on 25 April.
Two tortoises were stolen from a Northamptonshire pet store by a man who stuffed the reptiles down his trousers.