Councillors on Thursday voted 10 in favour, with one against and one abstention, for the warehouse and distribution centre on the Melton West business park, next to Long Plantation and the village of North Ferriby.
The nearest home to the facility, just off the A63, which will stand up to 25m high and operate 24/7, is just 50m away, the meeting heard.
Residents raised concerns including about air and noise pollution, heavy lorries parking up overnight for rest periods on nearby lanes and the noise of reversing HGVs late at night. In all there were 1,300 objections, with some objectors submitting multiple comments.
Many are concerned they will experience the same problems as people living close to other Amazon sites at Haydock and Hoo St Werburgh.
Ward councillor Julie Abraham told the committee "no amount of tinkering" would make the facility more acceptable, and they'd heard from health professionals, headteachers and police that it would "inevitably cause harm". She said: "This is an application that suits the applicants not the community or the environment."
There will be 2,288 two-way traffic movements a day to the site, widely believed to be for Amazon, which will have 55 HGV docking stations, 190 HGV parking spaces and 794 other parking spaces.
Coun Michael Lee who sits on the committee said 1,300 jobs generated by the facility would mean work for 1,300 families whether from North Ferriby, York or further afield.
Coun John Whittle said the site was designated for industrial development. Previous plans for 500 houses were turned down by the government in 2015.
But Coun Whittle said he thought it "absolutely inconceivable that a huge operator with masses of car parking space does not consider overnight lorry parking".
Another councillor, Geraldine Mathieson said a small percentage of spaces could be put aside as a "goodwill gesture" to residents and to help drivers coming to an end of the shift who may not be able to get to the lorry park at Goole 16 miles away.
However officers said the facility was run on a "just in time" basis and making it a condition of planning could see the facility's operation "unravel".
Instead the issue will be put down as an "informative" on the planning notice - as an additional comment to developers, but which is not enforceable.
The application will be delegated to officers for approval, following completion of an agreement on ecological mitigation.
Developers Wykeland Group welcomed the decision which they said would deliver a "huge boost" to the local and regional economy.
A statement added: "We will now work with council officers to conclude the agreement and address other conditions so that this important development can move into the construction phase.
"We look forward to working with the end user to deliver the development and the many benefits it will bring, including 1,300-1,500 permanent jobs, additional seasonal and indirect employment, and further jobs during the construction phase."