Deputy First Minister Nicola Sturgeon announced the funding, following agreement with the Scottish government.
The refurbishments to Queen St low level, Charing Cross and High Street stations will double the £1m programme of improvements already planned at 20 stations across Strathclyde.
Ms Sturgeon, who announced the investment on a visit to Glasgow Queen Street station, said: "Almost 20m commuters already use these three key Glasgow’s stations every year - this investment will deliver a £2m transformation of these, and other, stations, boosting capacity and improving accessibility.
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"The 2014 Games will be a huge event, attracting visitors from across the world, and these stations will be gateways to Glasgow as well as the Commonwealth Games.
"The appearance and service of our public transport networks is a hugely important part of that and all partners want to see that everything is done to ensure visitors and TV viewers throughout the world see an impressive image of Scotland."
ScotRail Managing Director Steve Montgomery said: "We have a host of improvements planned, including more seats and additional train services, as well as upgrades and enhancements at some of our stations. Our team will be working hard to ensure that we offer the highest standards of service to everyone who travels to the Games with ScotRail during Glasgow 2014."
David Grevemberg, Glasgow 2014 Chief Executive, said: "Glasgow 2014 welcomes the funding announcement made today by Transport Scotland. Queen Street Station will be a key entry point to the city for those who are attending the Games and looking to soak up the fantastic atmosphere that will be created."
Transport Scotland secured the funding boost from First as part of the five-month continuation of the rail franchise announced in December.
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