In debate lasting 17 hours across two days, councillors on Eastleigh’s Local Area Committee rejected the plans.
Now a final decision will be made by full council on April 8.
The decision has ramifications for the wider area are wide, the Solent Local Enterprise Partnership warned.
In a joint open letter penned before the meeting, chairman Brian Johnson and chief executive Anne-Marie Mountifield said refusing the plans would be be a ‘step away from an ambition to support the recovery the economy needs’.
After the meeting, Steve Szalay, operations director at Southampton Airport said: ‘Naturally, we are very disappointed with the lack of support (from the committee).
‘The committee did not support the recommendations of the planning officer and in doing so it has gone against the majority of Eastleigh residents who expressed their support during the consultation as well as the local business community.
‘However, this is far from over. We now welcome the opportunity to present our plans to the full council.’
He added: ‘We hope they will listen to the will of the people, the local business community and their own planning team and make the right decision for the future of the airport and seize the opportunity to create thousands of much needed jobs.”
Council members heard how the runway expansion would create more than 1,000 jobs, boost the local economy and result in a £15m investment.
But concerns were raised over the impact the move would have on noise and climate change.
The number of people affected by noise would go from 11,450 in 2020 to 46,050 in 2033, if the expansion goes ahead the meeting was told.
Officers said the mitigation measures proposed – including insulation and a cap on vehicles to restrict passengers to 3m per annum – would result in a ‘moderate adverse impact’.
During the debate Cllr Paul Bicknell, who backed the plans, said: ‘We have all taken this very seriously and it is difficult for all of us.
‘There is a very real risk that the airport is not viable.’
The airport breaks even at 1.2m passengers per annum and without the expansion it is estimated that it would have just over 1m passengers per year.
If the plans are approved the number of passengers could rise to 3m per year.
Cllr Alex Bourne said: ‘Whilst the report doesn’t say the airport is going to close, it is easy to read between the lines. It is not just a decision between health and wealth. We have an opportunity to save local jobs and create new ones.
‘It is a massive conflict between the health of many and the wealth of many by having a job.’