The Western Cape is in the third place with a pass rate of 82,7 percent‚ down from 85,9 per cent.
Motshekga also highlighted that no-fee schools had made their mark in the 2017 matric exams and out shown fee-paying schools by producing 76 300 bachelor passes compared to 67 867 from fee paying schools.
A total of 34 011 progressed learners wrote the requisite seven subjects during the 2017 NSC examinations.
This was according to the Democratic Alliance, who said in a statement on Friday that while the party congratulated the class of 2017, the "real" pass rate numbers were a cause for distress. The rest of the learners are modularising their examinations.
Even though Free State dropped by 2.2% from previous year, it retained its number one spot by being the best performing province and achieved 86%.
"We wish to thank all provinces, especially Gauteng, Free State, Mpumalanga, and KwaZulu Natal for the extra support and pointed interventions they gave to their progressed learners".
"If these provinces did not do this, some of the progressed young people, could have fallen through the cracks of the system, due to continuous repetition and ultimate drop-out from the system", said Motshekga.
"To the class of 2017, we have every confidence in our 2017 NSC candidates who have worked hard throughout the school year".More news: Senator Al Franken to Officially Resign from Office
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The issue of a common curriculum between public and private schools, as well as uneven development and unequal distribution of resources among the provinces, also needed urgent attention, it said.
She said 4 of the 70 districts achieved pass rates lower than 60%, adding that for the first time, no district has performed below 50%.
Education MEC Debbie Schäfer said it had been a "long, anxious wait for NSC candidates". Just over 28% of pupils achieved a pass that will allow them to go to university.
She said 68.7% of the candidates who wrote the 2017 NSC examinations passed and that the three provinces combined produced 44.8% Bachelor passes. Motshekga said the improved performance of the three provinces is a direct outcome of their targeted interventions.
South Africa is among the worst performers in terms of education internationally, having been placed last in Grade 8 Science and second-last in Maths out of 39 countries for the Trends in International Maths and Science Study (TIMSS) 2015.
Every year the DA raises concerns over the failure by the department to improve the retention rate of learners and it seems that there is little political will to improve retention rates.
Top achiever for learners with special needs holds his certificate awarded by Deputy Minister of Basic Education Enver Surty and Minister of Basic Education Angie Motshekga.
During 2017, 802431 candidates registered for the National Senior Certificate (NSC) exams.