The majority of the schools serve the east Belfast area.
Dundonald High School is to stay open, while Orangefield High School is to close by the end of the summer.
"With only 92 pupils remaining in Orangefield High School, it has declined to such an extent that it is no longer feasible to delay its closure," Mr O'Dowd said, in the Stormont Assembly on Tuesday morning.
"Regrettably this is an example where it has been left too late to turn the situation around, and the only reasonable option available to me regarding the future of Orangefield High School is to approve its closure from 31 August 2014."
He added: "In making this decision, I have advised the Belfast Education and Library Board of the need to work closely with schools which will receive Orangefield High School pupils to produce an action plan for improvement in educational outcomes."
Newtownbreda High School in south Belfast and Knockbreda High School in south-east Belfast are to amalgamate on 1 September.
Mr O'Dowd said: "I believe this will provide the opportunity for the development of a viable and sustainable school, initially on a split site.
"When the time comes to consider a new build, I want the South Eastern and Belfast Board to work together to determine the most appropriate location for the new school to allow it to serve the local population."
Ashfield Boys and Girls Schools have been refused an intake increase, while Priory Integrated College in Holywood, Co Down is to be allowed to increase its school population to 500 - a lower level than proposed.
It has been clear that change has been necessary in east Belfast. We must create a network of schools that serves pupils and communities and delivers a good education to every child. It was on this basis that I have carefully scrutinised the proposals and made my decisions.
Education Minister, John O’Dowd
Speaking on the development plans, the minister said: "The issues addressed in these proposals have clearly highlighted the need for area planning and, in particular, the need for managing authorities to co-ordinate and bring forward linked development proposals.
"Since the start of the area planning process, I have been clear that the challenge is to put the pupil at the centre of the decision-making process. The focus must be on pupils rather than institutions."
Mr O'Dowd added: "The young people of east Belfast deserve a quality education; they deserve the opportunity to fulfil their potential in school; and they deserve the chance to make the most of the life opportunities available to them."
East Belfast UUP MLA Michael Copeland welcomed the news that Dundonald High School will remain open.
He said that his sense of relief will be shared by the school's pupils, parents and teachers.
"There is no doubt that Dundonald High School has had a difficult time," he said.
"But, having witnessed the reaction of the local community once closure was mooted, I am confident that the will and determination exists to implement the changes necessary to turn things around and to ensure that the school can flourish and deliver high quality teaching and learning - and in so doing, raise the achievement and expectation of the young people of Dundonald.
"The importance of a good education in terms of career prospects and employment has never been greater.
"It is essential that we all act together to ensure that the pupils of Dundonald High School are provided with the high quality education which they both need and deserve, in order to fulfil their potential and acquire the skills necessary to compete in the job market of today and tomorrow."
First Minister Peter Robinson said: "The statement in relation to Dundonald High School will be warmly welcomed by all those in the school and the wider community who have campaigned so vigorously for the future of this school.
"We have consistently made the case for Dundonald's future and the seeds have already been sown for the ongoing work which will be required to ensure that the schools remains sustainable in the long-term.
"I would hope that the minister's very positive attitude in relation to Dundonald High School will continue and that the efforts by parents, pupils, staff and the community will be matched with the necessary back-up from the Department of Education."