A police spokesperson said two men carrying knives entered the Stanmore Road store in Linwood, about 11.20pm on Wednesday.
The store owner was punched and a quantity of cash and synthetic drugs were stolen. The shop owner's injuries were not serious.
Police stopped a car near the store and the two occupants of the vehicle were arrested. A third man is being sought by police.
A 30-year old man and an 18-year old man, both from Christchurch, were appearing in court on Thursday on aggravated robbery charges.