Train services were due to resume on the Onehunga line at 10.33am.
Commuters were advised to take the bus or travel by train to Penrose on the still operating section of the Southern Line then transfer on to a shuttle bus to get into the city.
There were still minor delays across the rest of the rail network nearly four hours after this morning's fault on the line between Newmarket and Britomart.
A plea was made to consider using alternative transport to get to work this morning.
The Herald's Lane Nichols was today travelling to the city on a train from Sunnyvale in West Auckland.
The 8.30am service came to a grinding halt at Grafton, two stops before Britomart.
Passengers were told by a guard the train would be delayed and he was unsure how long everyone would have to wait.
Passengers were allowed to get off to get some air while the train sat idle.
The train got under way again and after a 15-minute crawl between the Grafton and Newmarket stations the train was "flooded" with stranded passengers waiting on the Newmarket platform.
The train was "completely jammed" and headed for Britomart, Mr Nichols said.
Mr Nichols said his overflowing train eventually pulled into Britomart 15 minutes behind schedule.
Auckland Transport tweeted that trains on the Western, Eastern and Southern lines were now running at reduced frequency.
Scheduled buses were accepting rail tickets.
The train delays prompted one disgruntled passenger to launch an online petition demanding a free day of rail travel as compensation for major delays in recent weeks.
Frustrated commuter Sam Vernon said disruption to the rail network had been "diabolical" this week.
He said considerable delays and cancellations have led to much frustration for users.
"The network is close to unusable, the service is so bad.
"The line given by train staff is 'Talk to Auckland Transport', so we the users demand a day of free travel on the Auckland Transport Rail Network as compensation for the poor service this week," he wrote.
Auckland Transport said the delays were caused by a track fault, which occurred at 6.40am.
