Western Isles councillors have voted 18 to 13 to shut two small secondary schools at Bayble on Lewis and Daliburgh on South Uist.
Costs per pupil at Daliburgh School were "very high"
The vote, taken at a full meeting of Comhairle nan Eilean Siar, overturned the education committee's recommendation last week.
It had suggested any decision be deferred until a consultation concluded on other proposed school closures.
Scottish ministers, however, will have the final say on Daliburgh.
This is because of the distance pupils will have to travel to an alternative school.
Education officials had pushed for Bayble and Daliburgh to be shut because of costs and falling rolls.
The two schools provide S1/2 level education, before the pupils go to larger academies for the rest of their secondary schooling.
Parents have been campaigning to save the schools and others, including Paible, which have been earmarked for closure.