The organisation, which is responsible for operating and improving England's motorways and major A roads, rejected a shortlisted option to build a bridge or tunnel next to the existing Dartford Crossing.
Transport Secretary Chris Grayling will confirm the Government's preferred plan, which would be subject to planning permission.
It would run from the end of the M2 near Rochester, cross the river to the east of Gravesend and join the M25 between junctions 29 and 30.
Three potential approach routes have been identified north of the river in Essex and two south of the river in Kent. The tunnel has been estimated to cost between £4.3 billion and £5.9 billion.
An estimated 77,000 vehicles would use the link each day in its first year.
It would be the first new crossing of the Thames east of London since the Queen Elizabeth II bridge opened in 1991.
Steve Gooding, director of the RAC Foundation, said the Dartford Crossing, which is used for 50 million journeys each year, is a "regular source of misery for tens of thousands of drivers'' stuck in queues.
He went on: "This decision on the route for another crossing will be applauded by many motorists, for whom the tunnelling work can't start too soon.
"Drivers will hope ministers won't skimp on the design for the new crossing.
"With traffic on the motorway network predicted to soar in the years ahead, motorists will want reassurance that the scheme is as future-proof as possible and will add as much capacity as is practical.
"This will be doubly true if we have to pay for the privilege of using the new crossing as we currently do at the old one.''
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