Engineers worked "round the clock" over the weekend to upgrade signalling between King’s Cross station, Cambridge and Peterborough, the infrastructure body said.
It had faced criticism after some organisers of national sporting and cultural events complained were not informed of the August 24 and 25 shutdown until up to four months after the dates were agreed.
Those affected included tens of thousands spectators attending cricket’s Ashes Test at Headingley; York’s Ebor festival; rugby league’s Challenge Cup final; the Leeds Festival and the Edinburgh Festival.
Network Rail fails Yorkshire over Bank Holiday closureNetwork Rail said the work had "created a more reliable railway which is more resilient in times of disruption".
Engineers also worked on overhead power lines in readiness for improvements to the track layout and the power supply, which will take place at a later stage of their £1.2billion investment.
Work to renew a level crossing in Newark continued on Monday meaning that a reduced service ran.
This work has also now completed and will mean passengers will benefit from a more reliable railway and reduce the number of times maintenance at the crossing needs to be carried out.
Buses were put on as a replacement with a relief train running between Chesterfield and York on Sunday. when crowding was expected to be the worst.
Ed Akers, Principal Programme Sponsor for Network Rail, said: “Our engineers carried out a huge amount of work over the last three days and I would like to take this opportunity to thank travellers for their patience whilst this vital work took place and apologise for any inconvenience caused.
“A full train service has now resumed following work on the East Coast Upgrade, which is a huge investment into the railway and will bring significant benefits for all users of the route.
"Such significant upgrades do bring some unavoidable disruption and we do understand that this can be frustrating. We will continue to plan this work meticulously and do as much work as possible without affecting passengers, and when this is not possible, make sure we carry out multiple improvements at the same time.”
Further closures are planned from early 2020.
Network Rail and train operators have pledged to "keep passengers informed".