Interim chief executive Richard Pennycook acknowledged the sale as an important move for the group, which will streamline its operations and cut costs to try to reverse losses of £2.5bn in 2013.
Mr Pennycook said: "I am pleased that the agreement we have reached with Bestway reflects the quality of the business and the high level of interest from a number of bidders. Bestway is acquiring an excellent pharmacy business characterised by the quality and professionalism of colleagues and high levels of customer service."
The pharmacy business, which employs 7,000 staff, made profits of £33m last year through 770 branches.
The mutual's Scottish pharmacies are mainly confined to the central belt, but branches can also be found in Perth and Dundee.
Bestway may continue to run the pharmacies under the Co-operative banner for the next year and draw on "certain services" from the group for another 18 months under the terms of their agreement.
Bestway is one of Pakistan's most diverse business empires, overseeing the country's second largest cement producer and second biggest private bank. It has also built up the second biggest cash and carry business in the UK, serving 125,000 independent retailers and caterers through 64 warehouses. It runs around 600 convenience shops in England through the Best-One brand.
Group chief executive Zameer M Choudrey, hinted at further expansion of Bestway's pharmacy business due to increasing demand for healthcare.
The sale will be completed in October, nine months after the Co-op's former chief executive, Euan Sutherland announced the likely disposal of the pharmacies and 15 farms to help shore up the group's finances, heavily damaged by the near-collapse of its banking arm last year.
The Scot left his position in March following a bitter row with the mutual's powerful network of regional boards over proposals to reform governance in the wake of the crisis, triggered by the discovery of a £1.5bn black hole in the Co-operative Bank's balance sheet and a failed bid to buy 632 Lloyds branches.
The bank had to be rescued by Co-operative bondholders shortly afterwards as part of a refinancing package.
Senior figures at the bank who oversaw a 2009 merger with Britannia, as well as top regulators at the time, have since been subjected to public grillings from the government's Treasury Select Committee.
MPs have been scrutinising due diligence surrounding the ill-fated deal and the appointment of an inexperienced Methodist minister, Paul Flowers, as the bank's chairman that same year.
Since Mr Sutherland stepped down, the mutual's members have agreed to pass reforms that will see the 150-year old institution create a PLC-style board of directors.
It was also announced this week that the Co-op bank's newest chairman, Richard Pym, would leave in October to take the helm at Allied Irish Banks.