The move, effective from January, will see the allowance for Bill Winters and Andy Halford dropping to 10% from 20% of their salary, in line with industry standards, with the bankers settling for £237,000 and £147,000 pension allowances respectively.
The new policy will reduce the two men's maximum receivable bonus by 8%, as their bonuses cannot be over 200% of their fixed pay.
At the annual shareholders meeting held in May, 36% of shareholder votes were against a remuneration proposal to allow Winters to up his pension allowance on top of his £2.4mln salary paid in shares and cash.
“Picking on individual pension arrangements… and suggesting that there is some big issue there is immature and unhelpful,” he told the Financial Times in July, although the investment bank said on Friday both executive directors have accepted the change.
Analysts at AJ Bell pointed out the argument to pay executives generously in order to retain talent is valid when investors are also rewarded, however, the total return since June 2015 has dropped by 20.5%.
Standard Chartered shares were relatively unphased, just down 0.5% at 730.20p on Friday afternoon.