The Great North Rd and Rosebank Rd exits on the Northwestern Motorway and the Tristram Ave and Constellation Drive exits on the Northern Motorway also suffered delays.
SUNA Traffic Channel chief executive Adam Game said the Southern Motorway delays had to be taken in the context of overall traffic flows.
"It's a section of road that actually holds up quite well given the high volume of traffic that it has to channel every day but periods of congestion are almost inevitable."
Mr Game said SUNA, which provides traffic updates to personal navigation devices, used hundreds of millions of readings from fleet vehicles per week in New Zealand.
The average speed of a vehicle in the middle of the night was compared to speeds at various times of the day to detect congestion, including on urban arterial roads.
The company used a mix of private and commercial vehicles to track the congestion.
Mr Game said drivers who used compatible navigation devices to get traffic information could also anonymously contribute data back to SUNA.
"At the moment, it's not surprisingly the smaller part of the data that we derive.
"Although over time it will become the dominant source of information. The other sort of probe vehicles are commercial fleets.
"We enter into arrangements with commercial fleet operators - taxi companies, couriers - who are tracking vehicles for other purposes."
The NZ Transport Authority's regional traffic manager, Kathryn Musgrave, said the agency had introduced a number of significant changes to ease congestion.
These included plans for an additional fourth northbound lane on the Southern Motorway from the Ellerslie Panmure onramp through to Greenlane.
"The NZ Transport Agency continually monitors its network to ensure the traffic does flow as smoothly as possible, particularly during peak hours."
Simon Lambourne of the Automobile Association, which provides its own AA Traffic real-time monitoring service, said the motorway network needed to be completed.
"Until we actually complete the motorway network, we are going to have congestion.
"We cannot lose sight of the fact that we do have to invest in our roading network, just like we have to invest in our public transport.
"And we do have to invest in our arterial roads as well, because they are actually becoming defacto motorways in Auckland."
View NZ's most congested intersections in a full screen map