Contracts have been awarded for the Edinburgh to Glasgow improvement programme (Egip), which has risen in cost from £650 million to £741.5 million.
Much of the extra money will be spent lengthening platforms at Queen Street to meet passenger demand with longer trains and integrate the station with Buchanan Galleries shopping centre.
Egip was announced in 2009 to improve reliability, capacity and journey times between Scotland's two biggest cities.
The Queen Street redevelopment, which has more than doubled in price from £49 million to £120 million, is not expected to contribute to cutting journey times but will add to the "accessibility and ambiance" of the station and wider public realm, according to a full business case by consultants Ernst & Young.
The cost of electrifying the line via Falkirk to make trains faster has been cut by a fifth to £248 million. Land, infrastructure and contingency costs have also been adjusted.
Transport minister Keith Brown said: "I welcome the contract award on the core electrification of the route and the hundreds of jobs this will support.
"This announcement represents another hugely important milestone in the delivery of Egip and shows that we are pressing ahead with the improvements which will give Scotland a railway fit for the future.
"Passengers will experience the benefits of a faster, more comfortable and more efficient railway. But the whole of Scotland will also enjoy the boost to our economy and environment.
"This is why the Scottish Government is right to invest in our railways and infrastructure.
"I was delighted only last month to open the new £25 million station building at Haymarket - completed on time and on budget which has transformed facilities at one of our most iconic stations.
"We are charging ahead with the electrification of the Cumbernauld lines and I look forward to the introduction of electric services on this important route in time for the Commonwealth Games.
"This is further evidence of close collaborative working between Transport Scotland and Network Rail and the excellent progress being made with Egip.
"We're creating jobs, helping reduce Scotland's carbon footprint and increasing opportunities for inward investment.
"Since I announced the first phase of Egip in July 2012, we have further developed the original scope to include an even greater transformation of Glasgow Queen Street station and I am pleased to announce the publication of the Egip business case which takes that into account.
"This prudent and comprehensive assessment of the investment case for Egip demonstrates substantial benefit for Scotland and its rail users, and that the first phase can be delivered on time and on budget."
Egp was a key transport priority in the SNP's manifesto for government in 2011, which pledged to deliver "services of just over half an hour" at a cost of about £1 billion.
Mr Brown hailed "hundreds of millions of savings for the public purse" when the cost was cut to £650 million in a 2012 strategic review, which recommended a phased reduction of journey times to make Egip's goals "more affordable and achievable".
Journeys of at least 42 minutes, rising to 44 mins at peak time, are now expected by 2019 and shorter 37-minute journeys are expected by 2025, according to the full business case.
The redevelopment of Queen Street is not expected to contribute to improved journey times.
The full business case states: "The redevelopment of Glasgow Queen Street station will allow the introduction of longer trains to provide the required additional capacity.
"Appraisal of redeveloped stations outside Scotland has comprised journey time savings through reduced walk time. These will not apply in relation to the proposal for the new Queen Street Station.
"Therefore, there is no available evidence to allow the assessment of benefits in relation to the station redevelopment.
"However, Queen Street is one of Scotland's busiest stations, occupying a prime position on the corner of George Square and the redevelopment will align with the extension of Buchanan Galleries shopping mall.
"The redevelopment of the station will, thus, be likely to deliver additional benefits which have not been captured in this analysis."
These include improvements in the "accessibility and ambience" of the station, improvements in "the public realm" and the creation of "significant retail benefits" for Buchanan Galleries.
"The benefits, if monetised, would increase the over present value of the benefits of Egip," it adds.
Labour transport spokesman Mark Griffin said: "While the publication of this business case is better late than never, I am still baffled as to how Keith Brown can claim this project is 'on track' and 'charging ahead' when it has been delayed and scaled back almost beyond recognition.
"Large parts of important information have been removed from the public version, which makes me wonder what else the SNP government are trying to hide.
"Keith Brown's previous commitment to full delivery has also been replaced by a vague assertion that ministers will take a view sometime in the future on when phase 2 will be delivered. It's a shambles.
"The focus now has to be on delivering what is going ahead, so that Scottish businesses can gain some benefit from improvements to the rail network between our two biggest cities.
"Yet there is still no concrete work plan to deliver the different phases. This must come forward so that those affected by the works can make plans.
"Under the SNP there has been a distinct lack of leadership on large transport projects with Audit Scotland criticising a lack of accountability.
"We know Nicola Sturgeon is preoccupied with independence but she has to take some responsibility for her day job and ensure that there are no more delays or changes to Egip, and that it is completed as quickly as possible."
Conservative transport spokesman Alex Johnstone said: "The Scottish Government has already scaled back on their original plans for Egip.
"Now, we find the costs rising to almost three-quarters of a billion pounds for a project completely lacking in ambition.
"For all the SNP's moaning about the problems associated with the Edinburgh tram project, their inept handling of this rail programme is rapidly becoming their own personal equivalent.
"For frustrated passengers, the prospect of having to wait almost a decade for real reductions in journey times - on what is supposed to be Scotland's flagship rail service - is a real blow."