"The examinations were conducted well, with no major incidents affecting the integrity or credibility of the examinations," spokesman Elijah Mhlanga said.
"The Minister of Basic Education Angie Motshekga says she is satisfied that the examinations have been conducted with integrity and without serious problems, despite the threats of protests in some parts of the country."
Mhlanga said that three weeks ago, protesters in the Eastern Cape threatened to disrupt the exams and police had to relocate matriculants from one school to another.
Exams across the country started on October 27 and ended on Friday.
A total of 688,660 candidates were registered to write the year-end examination.
Marking of the papers would start on Sunday, with 41,000 markers and 118 marking venues.
"The marking of the 2014 [National Senior Certificate] examinations will be concluded across all provincial education departments by December 18, 2014," said Mhlanga.
The marks would then be captured on the department's computer system, in preparation for the Umalusi standardisation processes, which would take place from December 21 to 23.
Umalusi, the Council for Quality Assurance in General and Further Education and Training, moderates the educational systems and processes.
Motshekga is expected to announce the exam results on January 5. Pupils will get their results on January 6.
On Tuesday, the department said the matric results published in newspapers would reflect only pupils' identity and exam numbers and not their names.
This was decided after a task team recommended that the practice of publishing individual names be reviewed.