The announcement, made at 8am this morning, would have meant residents living nearby being rehoused.
2,300 objections from tenants and community leaders were put forward in a public inquiry in September.
Mr Jones said: "In reaching my decision I have taken account of the concerns raised by the inspector that the overall size of the scheme would have a significant impact on the landscape and would affect walking and cycling routes.
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"I have also noted his remarks that while he considers that this section of the A494 will need some form of improvement in the foreseeable future he considers that the scale of the scheme as originally proposed is greater than required.
"After careful consideration, I have taken the decision that the published draft orders for the A494 Drome Corner to Ewloe scheme will not be made."
Alyn and Deeside Labour AM Carl Sargeant said: "This is great news for local residents.
"The proposed changes to the road would have had a terrible impact on the quality of life of local people and the environment here. It is the right decision."
(CD/JM)
