It comes as the group revealed a 23 per cent profits plunge.
Workers at the group will now receive 2 per cent of annual salary as bonus pay.
While cutting the staff bonus, new chairwoman Dame Sharon White stopped short of axing it altogether despite her predecessor, Sir Charlie Mayfield, warning in January that employees may miss out.
John Lewis staff impacted by closures will be "actively supported" should they wish to stay working for the partnership, the group said.
Chairwoman Dame Sharon White - who took the helm at the group behind John Lewis department stores and Waitrose supermarkets last month - outlined a plan to return the group to profit growth.
With measures including "right sizing" the group's store estate and slimming down its head office.
The group announced stores at Helensburgh in Scotland, Four Oaks in the West Midlands, and Waterlooville near Portsmouth will all close as part of the overhaul.
Dame Sharon said the measures were needed to reverse "profit decline" within the business.
She said: "This will require a transformation in how we operate as a partnership and could take three to five years to show results.
"We are stepping into a vital new phase for the partnership and I have no doubt we will come through it stronger."
There was, however, some cheer for the group. Dame Sharon unveiled plans to invest in Waitrose online, ahead of its tie-up with Ocado ending in September, with plans to hire 2,400 new staff and build a new fulfilment centre in Enfield, north London.
The strategic review is expected to be completed by the autumn, but bosses stressed the group would remain employee-owned and keep its two brands - John Lewis and Waitrose.
Dame Sharon described the current climate as "the most challenging but exciting times in retail for a generation."
The partnership's results show the third consecutive year of falling annual profits.
The John Lewis chain recorded a £37 million statutory loss last year, against earnings of £92.6 million the previous year.
Waitrose delivered stronger results, however, with a 6.4 per cent rise in earnings to £211.9 million.
It came just three months after the managing director of Waitrose, Rob Collins, also stepped down following a major restructuring.