The rise, which MSPs do not vote on, is linked to public-sector rises in Scotland using the annual survey of hours and earnings published by the Office for National Statistics (ONS).
It means members will receive an annual salary of £64,469 - up by a total of £890 on the current £63,579 per year.
The salary entitlement for the First Minister, including MSP salary, will rise by a total of £2,179 to £157,859.
But Scottish Government ministers will continue to freeze their pay at 2008-2009 rates.
Frontbench members do not take their full salary entitlement, having pledged not to do so for the duration of the Parliament.
It means the First Minister will continue to earn £135,605.
The entitlement for Cabinet secretaries will rise by £1,559 to £112,918, including their salaries as MSPs.
With the freeze in place their pay will be £96,999.
Ministers' salary entitlement will increase by £1,309 to £94,819.
Additional money raised by the pay freeze will be made available for public spending.
Details of finances at Holyrood were set out by the Scottish Parliamentary Corporate Body (SPCB) at the Finance Committee on Wednesday.
At the committee, the SPCB also confirmed the budget set for office holders will also rise, driven in part by an increase in the demand for business during the Parliamentary session.
Scottish Liberal Democrat MSP Liam McArthur, a member of the SPCB, said: "There's no getting away from the fact that demand of business in this place (Parliament) has only increased.
"This session is the session with the largest number of Member's Bills, of Parliamentary questions, of motions, of business within committee and within the chamber.
"And added to that obviously there's been the additional pressures put on business through the Brexit process."
He added: "We've sought to make efficiencies where we can but it's the responsibility of the corporate body to make sure the functioning of the business of Parliament is run as efficiently and effectively and as smoothly as possible, and that's inevitably involved us taking on additional resources to make sure that we are able to support MSPs and staff in the way that they would expect."
A Scottish Government spokesman said: "In 2020-21, Scottish ministers will freeze their pay for the 12th year running, recognising the wider economic and fiscal pressures, as well as the constraints placed on public-sector pay and increased living costs more generally.
"So long as these constraints remain, we believe it is right to maintain the ministerial pay freeze.
"Since April 2009, the ministerial pay freeze has made over £860,000 in additional funding available for public spending."