The proportion achieving A* to C grades in both maths and maths numeracy exams was 46.1%.
The first tranche of more than 20,000 pupils sat the papers last November.
The new qualifications started being taught in 2015 and were brought in as part of reforms to improve numeracy standards.
The chief executive of exam board WJEC Gareth Pierce said:  "Students and teachers in Wales should be extremely pleased with the successes demonstrated by the results in both these new qualifications."
Mr Pierce added: "There is of course plenty of time remaining within Year 11 for those candidates who wish to aim for improvement on the grade achieved on this occasion."
Schools started teaching the new qualifications in September 2015 and the majority of pupils will sit them, as usual, in the summer.
The GCSE numeracy qualification assesses the maths that pupils will need in their everyday lives, at work and in other subject areas in school.
More than 12% of nearly 29,000 pupils who took the exam achieved the very top A and A* grades.
The GCSE mathematics exam involves aspects needed for scientific, technical or further maths study.
About 10% of the 22,686 pupils who took this exam got the highest A and A* grades.
Education Secretary Kirsty Williams also congratulated the students and said the "made in Wales" qualifications were aimed at raising standards by placing a sharper focus on literacy and numeracy.
"The new qualifications are part of extensive reforms to our education system to give our young people the right skills and knowledge to thrive in the modern word," she said.
"Our national mission is to raise standards and make sure everybody has a chance to succeed."
They are being called "significantly different" from the old GCSEs, with warnings about taking care when comparing them with previous results.
For the whole of the last academic year, 65.5% of 16 year olds got A* to C grades.

4 October 2016 Last updated at 10:16 BST
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