Transport Scotland announced the rise which applies to all services on the network, including season tickets and flexipasses.
It also announced the removal of peak time fares pilot will be extended for another three months until June.
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Caledonian Sleeper fares will increase on average by 8.7% from January 1, excluding seated tickets.
Transport Scotland said Scottish Government ministers have agreed the new fares “after lengthy consideration to ensure rail services are sustainable in the longer term and that budgets align with the overall funding available”.
Fiona Hyslop, Minister for Transport, said: “The Scottish Government rightly made the decision to freeze flexi-pass and season ticket prices as part of its response to the cost-of-living crisis. While this has now remained in place for almost two years, it is simply no longer sustainable.
“We know that any increase is unwelcome for passengers, therefore we have kept the rise as low as possible to maintain the attractiveness and affordability of rail as a travel option.”
“We continue to look at ways to encourage greater rail use and that is why we are extending our peak fares pilot for a further three months until June 2024.”
Rail unions said the rise was a ‘slap in the face’ for travellers.
Kevin Lindsay, ASLEF’s Scottish regional organiser, said: “It is little wonder the Scottish Government is sneaking this news out a day after the budget.
“It is an outrageous slap in the face to Scotland’s travelling public and is in stark contrast to the Government policy of supporting a shift from road to rail.”
Opposition politicians also criticised the hike.
Graham Simpson, Scottish Conservative transport spokesperson, said: “This rise is well above the falling rate of inflation and is a body blow to passengers.
“It does nothing to help hard-pressed Scots who are reeling from the SNP’s catastrophic budget cuts.
“It will do nothing but deter people from travelling by train. It is the opposite of what we should be doing.”
