The firm had planned a 16-day shutdown of 12 miles of the line just north of London in August and a further nine-day closure in February next year.
The improvement work was originally planned as part of a £9 billion upgrade of the line a decade ago, but shelved to save money.
Network Rail said today a “detailed review” of the £81 million scheme to renew track, junctions, signalling and upgrade overhead power lines had found such long closures were no longer necessary.
The project will now go ahead over three weekends in August and two in February 2015 - in addition to during previously planned weekend closures in May, December and April 2015.
Network Rail route managing director Dyan Crowther said: “We have been able to develop a revised schedule of work at Watford that will cause less disruption for passengers.
“There is never a good time to close the railway, and removing these two significant closures means we will have to carry out the work over eight separate weekends and Bank Holidays, which will still impact on journeys.
“However, the feedback from passengers suggested this was a preferred situation.”
Guy Dangerfield, of watchdog body Passenger Focus, said “Passengers will be enormously relieved the West Coast route will not now be closed at Watford for days on end in August 2014 and February 2015”.
Phil Bearpark, operations and customer service director for Virgin Trains, which operates cross-Border services on the line from Glasgow and Edinburgh, said: “We welcome the news Network Rail has created a plan that will not involve a 16-day closure in August or a nine-day closure in February, which would have had a significant impact on all our customers.
“Although the new plan now largely involves weekend and bank holiday closures, we are still aware many customers will be affected and we are working with industry partners to offer sensible alternative travel routes.”