The government said the lifeline funding would "help secure the future" of the King's and Festival Theatres in Edinburgh, Eden Court in Inverness and Aberdeen's Music Hall, Lemon Tree and His Majesty's Theatre venues.
The five venues, which are understood to have made direct pleas for financial help to the government recently, have already had £3m worth of support since being forced to close their doors last March.
They are believed to be the first arts organisations in the country to benefit from a new £185 million pandemic support package for businesses which was announced by Scottish finance secretary Kate Forbes last month.
The government said the awards had been made based on the “current trading position” of the operators of the five venues, adding: “The scope of each fund was decided by the Scottish Government, based on advice given by Creative Scotland.”
The government has already pledged that an extra £4m will be ringfenced to support grassroots music venues, while the independent museums sector has been allocated £3.1m.
Eden Court, which had previously secured £1.27m in government funding, has been allocated another £800,000.
Aberdeen Performing Arts, which runs the three city centre venues, has been awarded £1.4 million on top of the £980,000 it was previously given.
The Capital Theatres trust, which runs the two Edinburgh venues, has received an additional £800,000. It had previously secured £750,000.
Scottish culture secretary Fiona Hyslop said: “This funding will help to secure the future of three of Scotland’s important independent performing arts charities, protecting jobs and addressing some of the financial pressures they are facing.
“These venues all receive UK and international touring work of major scale, make a significant contribution to the economy and support a network of arts organisations, artists and creatives at the heart of our cities and regions.
“The Scottish Government has allocated more than £120 million of additional funding to support culture and heritage since the start of the pandemic and we will continue to listen to the needs of the sectors.”
Fiona Gibson, chief executive of Capital Theatres, said: “Losing over 90 per cent of our turnover as a result of the pandemic has been a truly staggering experience.
"We would like to thank the Scottish Government for continuing to support Capital Theatres through these challenging times.”
James Mackenzie-Blackman, Eden Court’s chief executive, said: “All of us at Eden Court are immensely grateful to the Scottish Government for this life-line support.
"Together with the communities we serve, and with the artists of the Highlands and Islands, this support will allow us to continue fulfilling our mission to bring the world to the Highlands, and the Highlands to the world.”
Jane Spiers, chief executive of Aberdeen Performing Arts, said:
“This funding will go a long way towards helping us survive, thrive and play our part in the cultural and economic recovery of the north-east.
"As an arts charity with a high reliance on earned income and over 500 show cancellations to date through 2021 and into 2022, it provides us with a vital lifeline.
“This new funding recognises the unique scale of the challenge facing large-scale theatres and concert halls, the significance of culture to the region’s economic future and the vital role we play in civic, cultural and community life.”