The £300m re-signalling project affected Cardiff and Valley line services and mainline travel between Newport and Bridgend from Christmas Eve until 2 January.
Passengers experienced "severe delays" and cancellations from Thursday after engineering works over ran.
Network Rail said the lines have now been handed back to rail operators.
The project also saw a new platform eight open at Cardiff Central station on Monday - which will allow more trains to arrive at the station at any one time.
It has been designed to ease congestion and will be used by passengers travelling on lines to Penarth, Barry Island and destinations in the Vale of Glamorgan.
The positive effects were already being felt by commuters on Tuesday.
Peter Clarke, who lives near Reading but stays in south Wales during the week while working in Cardiff, even missed work over the festive period as he was worried about the effects of rail alterations.
The works on top of weekday train delays meant he "couldn't face it" and he lost wages.
He described the situation frustrated passengers faced before platform eight opened - sitting on a static train waiting for a platform to become free.
Mr Clarke said: "If I'm staying in a hotel in the valleys, it is not too bad to Queen Street. But then to central, a three or four minute journey can take 15 to 20 minutes, just sat between the stations.
"It is so frustrating, it is quicker to get off at Queen Street and walk."
He said the situation is exacerbated if a train is late, with trains then queuing to get on to one of the few available platforms.
But with platform eight open, allowing more to arrive at central at the same time, he said he had a "good experience" on Tuesday.
Jacob Hewlett, 24, has been left frustrated by late trains, but believes the situation will now improve.
He said: "I travel on the Ebbw Valley line and there are always plenty of delays - 20 or 30 minutes into Cardiff.
"It is just really annoying when you have another 10 or 15 minutes on top of that after a hard day's work. An extra line should make my trip to work an awful lot easier."
Ryan Smith is also confident the work will improve train speeds, but wants to see more work done nearer his home.
The line to Treherbert turns to a single track north of Porth, which means only one train can travel on it at a time.
He wants to see another put in to speed up the service near the end of the line.
For Louis Curtis from Penarth, securing investment to improve the front of the station is just as important as improvements inside.
He described the entrance as "a bit grotty", adding: "Before you had the bus station outside, which wasn't that nice.
"Now, it's been knocked down and work is going on, it doesn't give a good impression of the city.
"Hopefully it will be better when everything is done, but there should be more green spaces."
Natasha Higgitt, 20, uses the line to Cross Keys mid-morning on weekdays and said it is fine at that time, but believes the new platform will improve the situation at rush hour.
Meanwhile. on Tuesday protests were held at stations across the UK over a rise in rail fares, including Cardiff Central, Aberdare, Abergavenny and Merthyr Tydfil.
An average price increase of 2.3% was introduced on Monday covering regulated fares, including season tickets, and unregulated, such as off-peak tickets.
The UK government said it was delivering the biggest rail modernisation programme for more than a century.
Speaking to BBC Radio Wales outside Cardiff Central station, Owen Herbert from the RMT union said the rise in fares was an "absolutely disgrace" and was not reflected in the services.
"The services have been depleted while fares have been going through the roof," he said.
He called for the railway system to be nationalised so money taken in fares is "fully reinvested into the services available to the passenger."
Work to upgrade the rail lines in south Wales has been completed over the festive period, Network Rail has said.