It came in a report which also named Scotland’s ten most gridlocked roads last year - split evenly between Glasgow and Edinburgh.
In Aberdeen, drivers were at a standstill a quarter of the time and move at an average 5.5 mph.
The Granite City was rated as the overall third most congested in the UK after London and Manchester, with Edinburgh fifth and Glasgow 11th.
However, Glasgow had Scotland’s three most congested roads.
The A82 Great Western Road in Glasgow topped the list, where traffic averaged less than 13mph between St George’s Cross in the city centre and Anniesland.
Second was the M74 northbound between junctions three and eight in the morning peak, where motorists averaged 34mph - in perhaps a reflection of the major roadworks on the motorway.
In third place was the M8 westbound through Glasgow city centre between junctions 13 and 22, where traffic only averaged 29mph in the afternoon rush hour.
Edinburgh’s worst tailback was on the A1 and A199, from the A1 junction with the city bypass to Baltic Street in Leith, where vehicles averaged 25mph in the morning peak.
Drivers averaged 16mph in the afternoon peak on the A8 westbound between Haymarket and the Drumbrae roundabout in Corstorphine.
In Aberdeen, the opening of the western peripheral route (AWPR) next winter is hoped will significantly cut congestion.
It cost them £1,300 each in lost time last year, compared to £1,009 in Edinburgh and £766 in Glasgow.
INRIX, which analyses GPS data from vehicles, said congestion levels had improved in Aberdeen, Edinburgh and Glasgow since 2015 but detailed comparisons were not available because of changes to measurements.
It said congestion cost the three cities a combined £582 million in 2016, and an estimated £2.4 billion across Scotland.
Chief economist Dr Graham Cookson said: “Aberdeen has incredibly high congestion at peak hours. It’s a very dense city with many people commuting from rural areas.
“Despite Brexit, 2016 saw the UK economy remaining stable, fuel prices staying low and employment growing to an 11-year high, all of which incentivises road travel and helped increase congestion.”
Neil Greig, the policy director of the IAM RoadSmart motoring group, said public transport must become a more attractive alternative to drivers sitting in queues.
He said: “Nearly all of the congestion black spots have substantial public transport alternatives available, but they have clearly failed to attract car users out of their vehicles.
“For as long as our buses and trains continue to be overcrowded, unreliable, uncomfortable, slow and expensive, drivers will be tempted to sit tight in the daily grind.
“Not only is this costing the economy millions of pounds but the environmental problems are building up as well.
“Public transport planners need to provide services that make it easy to leave the car at home or at the local park-and-ride, but on to many routes that option is still not available.”
“In Aberdeen, ironically the long-awaited AWPR will open soon, just when the economy is taking such a hit from the contraction of the oil industry.
"Maybe next year we will find Aberdeen is one of the least congested cities, but that will be very little consolation to those who can no longer afford to drive.”
Aberdeen City Council regeneration and transport convener Ross Grant said: “This report highlights what we have been saying for years, that without adequate funding from the Scottish Government it is really difficult to make decent improvements to our roads.
“The council has spent significant money in building a new third Don crossing, contributed £75 million to the AWPR and is looking at other options to try and ease traffic congestion.
“Aberdeen has been badly let down by the Scottish Government which promised ten years ago to upgrade the Haudagain roundabout, but has still failed to move forward with the project.”
A spokesman for the Scottish Government’s Transport Scotland agency said: “Our total investment in motorways and trunk roads has risen from £830 million in 2016-17 to £997 million, which includes major improvements such as to the M8/M73/M74.
“The Scottish Government has treated local government very fairly despite the cuts to the Scottish Budget from the UK Government.
“Aberdeen City will receive an additional £12.2m.
"We are investing £745m in the AWPR and progress is also being made with improvements to the Haudagain roundabout, with the recent publication of the Made Orders for the scheme.”