Figures show the overall pass rate for the controversial National 5 qualifications, which replaced Standard Grade this summer, was 81.1%, broadly similar to equivalent qualifications from the previous year. The pass rate for the lower National 4 qualification was 93%.
However, overall pass rates at Higher dropped from 77.4% last year to 77.1% - while those at Advanced Higher slipped from 82.1% to 81%.
The results, published today by the Scottish Qualifications Authority (SQA) as pupils receive their results through the post, follow a year of turmoil.
Staff argued the implementation of Nationals was rushed and confused. Teachers also warned pupils were subjected to an assessment overload, resulting in a significant rise in workload.
But Schools Minister Dr Alasdair Allan said Scottish education had taken a "significant step forward".
"The new Nationals represent a shift towards deeper learning and a greater emphasis on analysis, engagement and understanding. These are the qualities on which we will continue to strengthen our education system," he said.
Dr Janet Brown, chief executive of the SQA, paid tribute to the hard work of all staff involved in the development and introduction of the new Nationals.
She said: "I would like to give special thanks to all teachers, lecturers, parents, carers and SQA staff for all their hard work and commitment in developing and implementing the new system.
"There has clearly also been a tremendous amount of work put in by candidates, which has been rewarded."
Larry Flanagan, general secretary of the Educational Institute of Scotland, said pupils and teachers had delivered in a difficult set of circumstances.
"Scotland's pupils and teachers deserve high praise for a strong set of exam results that have been achieved during a very significant period of change for Scottish education," he said.
"It is gratifying to see the positive attainment rates in the new National qualifications, particularly in light of the challenging circumstances in which these new courses were introduced."
However, while the pass rates were generally welcomed, there was renewed concern over figures that show the number of exams Scottish pupils are enrolling for has dropped sharply following the introduction of Nationals.
Some 55,000 fewer entries were recorded in 2014 compared to 2013. This has fuelled fears some subjects are being squeezed out.
The issue has arisen because Standard Grades were studied over two years, but new exam courses are being taken over one year, leaving some schools with too few teaching hours to fit in more than six subjects.
Eleanor Coner, a spokeswoman for the Scottish Parent Teacher Council, said: "We have had very varied comments from parents, but some have expressed a worry about the lack of exam choice.
"We need to keep a close eye on how it develops to make sure youngsters across Scotland can get the full range of choices of qualifications that they want."
Graeme Logan, strategic director at curriculum body Education Scotland, said changes to the pattern of entries was expected under the new Curriculum for Excellence (CfE).
He said: "As schools implement CfE some young people are studying fewer subjects so they can study them in greater depth and develop more knowledge and understanding.
"Across the senior school they have more flexibility to take different qualifications at different times and they can also bypass lower level qualifications and spend more time studying for higher qualifications."
The SQA figures also showed pass rates for Higher and Advanced Higher falling for the first time in nearly a decade.
However, Moyra Boland, director of learning and teaching at Glasgow University's School of Education, stressed the slight decline should not be a concern.
She said: "Any exam system where pass rates rise year on year over a long period of time can be open to accusations of manipulation, whereas what we are seeing here is reflective of a robust and transparent process.
"There has to be a period where exams results drop to reflect the natural fluctuations of a system where stringent criteria are being applied in exactly the same way every year. When that happens it creates greater confidence in the system and subsequent rises are seen as genuine improvements in standards."