Fierce community support was not enough to save Clapham & Patching Primary, in Worthing, and Rumboldswhyke Infants, in Chichester, both of which the council felt were financially and educationally unviable.
Closure notices will now be issued to both schools.
The move comes despite a council scrutiny committee asking for the proposals to be dropped last week.
Andrew Griffith, MP for Arundel & South Downs, had written an open letter to the council appealing for the Clapham & Patching plans to be dropped.
After the decision was made, on Wednesday (April 22), he said: “This is the wrong decision made with distasteful timing and I deeply regret its impact on pupils, parents, staff and the local community.
“The decision is contrary to the recommendation from the council’s own scrutiny committee, the government’s policy of keeping small rural schools open and in the face of a credible alternative put forward by the well-regarded team at Worthing High School.”
Sarah Sharp, Chichester District councillor and chairman of the Friends of Rumboldswhyke School, said she and many others were devastated by the decision.
Mrs Sharp added: “Not only that, but we are confused by what seems pure ineptitude.
“At least three councillors voted to close the school but hoped it would then find success in its offer of academisation under Bishop Luffa. How does that work?
“This is the second time that the cabinet has voted to overturn recommendations to save not only Rumboldswhyke but also Clapham and Patching. We still don’t know why. But we do know that something feels very wrong.
“We are considering all options, including a legal challenge.”
Deborah Urquhart, cabinet member for environment, was one of the councillors who showed support for the schools during the scrutiny meeting.
She was told she could not take part in the cabinet’s discussion or vote as she was considered to have ‘pre-determined’ the issue.
Such an accusation had been fired at the council by Jamie Fitzjohn (Con, Chichester South).
At the scrutiny meeting, Mr Fitzjohn said the council had ‘influenced and manipulated’ outside bodies, such as Ofsted, to get want it wanted.
While this was vehemently denied by Paul Wagstaff, director of education and skills, he did acknowledge that the wording of an email sent to Ofsted on April 29 2019 ‘to try to defer’ an inspection was ‘inappropriate probably’.
In an effort to ease the coming changes for children with special needs, members agreed that the school buildings at Clapham & Patching and Rumboldswhyke should be kept open to allow them to attend lessons while their parents decided on a new school.
The cabinet also agreed recommendations for three other schools – Stedham Primary, Warninglid Primary, and Compton & Up Marden Primary.
All three are in the process of forming federations with other schools, with Warninglid scheduled to move from Haywards Heath to Pease Pottage by September 2021.
Karen Dunn , Local Democracy Reporting Service