Pick n Pay, which also owns discount supermarket brand Boxer, was also prohibited from selling general merchandise and hot foods.
Restrictions were lifted mid-May and subsequently from June 1, but tobacco sales have been prohibited throughout, and the ban on alcohol sales was reinstated last month.
The retailer said headline earnings per share (HEPS) for the 26 weeks to Aug. 30 would be down more than 42.52 cents from 85.03 cents reported in the previous year.
Shares in the company were down 5% at 0737 GMT.
It also blamed Covid-19-related costs for the decline in HEPS, the main profit measure in South Africa that strips out certain items.
The group launched a voluntary severance programme in March, through which it said more than 1,400 employees have left the business.
Reuters