The group said it will reduce the renowned bonus to three per cent of annual salary, with 83,000 partners sharing out a pot worth £44.7m, down from £74m the previous year.
It has cut the bonus for six years running now, and the latest figure is down from five per cent last year. It comes as John Lewis announced in January that it would be closing its Southsea store Knight and Lee in the summer.
The partnership, which includes upmarket supermarket Waitrose, warned in January that it might have to axe the renowned payout for the first time since 1953 as it battles challenging trading conditions.
It came as the group saw profit before tax, exceptionals and bonus plummet 45.4% to £160 million.
While overall revenue climbed one per cent to £10.3bn for the period ending January 26, operating profits were down sharply due to challenges at John Lewis.
Operating profit at the department store fell by 56 per cent to £114.7m due to weaker home sales, tighter margins, higher IT costs and the cost of new shops.
Like-for-like sales at the brand were down 1.4 per cent.
In contrast, operating profit at Waitrose recovered, climbing 18 per cent to £203.2m. The supermarket's like-for-like sales jumped 1.3 per cent.
Chairman Sir Charlie Mayfield said: ‘In line with expectations set out in June, our Partnership profits before exceptionals have finished substantially lower in what has been a challenging year, particularly in non-food.’
He warned that trading conditions are set to remain challenging in 2019, but that the partnership was ‘confident in our strategic direction and customer offer across both brands’.
When stripping out exceptional items and the bonus payout, pre-tax profit was up 9.2 per cent at £117.4m.
The firm also said that it will sell off five Waitrose stores to rival retailers, adding that staff at those outlets have been informed.
Sir Charlie added that Brexit and retail failures are taking their toll.
‘Near-term uncertainty, politically and in the economy, is having a major impact on consumer confidence, but we do not believe the market conditions are cyclical.
‘The disruption we have seen on the high street, including business failures and renewed interest in mergers and acquisitions, are instead signs of an inevitable market adjustment which will require greater clarity on whether brands are competing on scale or difference.’
The Partnership also warned over a no-deal Brexit - or ‘unmanaged transition’ and the resultant impact on consumer confidence and trade.