In addition they endorse proposals to make over-16s in England study GCSE maths until they have achieved at least a C grade.
It says more than 10, 000 pupils missed out on a C grade in GCSE English because of what they have called a "statistical fix".
Examiners raised the mark needed for a GCSE English C grade based on their judgement of the quality of the work, lawyers for the examiners have said.
The group argues the issue is particularly acute because of the critical importance of achieving a C grade in GCSE English for future educational and professional opportunities.
Meanwhile, the National Union of Teachers (NUT) says an independent review should establish how many pupils who were on course for a C grade got a D.
On Wednesday, lawyers for the exam boards told the court they had raised the mark needed for a GCSE English C grade based on their judgement of the quality of the work.
The challenge centred on more than 10, 000 pupils who missed out on a C grade in GCSE English, which is a crucial benchmark used for entry into further education, vocational training and employment.
But a C grade or above in GCSE English is also a key element on which national league tables are based, increasing pressure on teachers to ensure their students get the best results possible.
He added that AQA had reneged on guidance to schools about the standard needed to achieve a C grade and said that this had hit the most vulnerable part of the student population hardest.
This will aim to bring all pupils up to at least a C grade at GCSE, but for pupils who cannot achieve this the government is proposing "high-quality alternatives", which will be identified after a consultation.
Pupils who were given a D grade rather than the expected C grade could mean that difference between staying on at school or dropping out and becoming a Neet, said Kenny Fredericks, head of George Green's School in east London.
The case centres on more than 10, 000 pupils who missed out on a C grade in GCSE English which is a crucial benchmark used for entry into further education, vocational training and employment, but the decision affected all the grade margins.
They will say that between January and June 2012 it was decided that too many students were going to get a C grade or better in GCSE English, so a decision was taken to push up grade boundaries for the exams marked in June to bring down the numbers of good grades for the year as a whole.
But, on appeal, the offence was reduced from Grade C to Grade A after the tribunal viewed a video showing the incident from a different angle to the ones presented at the original hearing on Tuesday.
You can get a "C" grade at the Yale School of Management and still launch FedEx.
It called for June's papers to be regraded in line with the January C-grade boundaries.
It resulted in a slight fall in the number of pupils achieving at least a C-grade, from 65.4% to 63.9% this summer.
Obtaining a C-grade in GCSE English is a crucial benchmark required for pupils wanting to continue their studies at A-level or further education college.
An alliance of heads and teachers' unions is continuing to press for June's papers to be regraded in line with the January C-grade boundaries.
"Further it has been reported that some students are often 'coached' to a C-grade at AS and A-level rather than attempting to produce higher quality answers, " it said.
Some have more students in the C-D grade range and have therefore been affected more than others.
Overall English GCSE results at grade C and above were down by 1.5 percentage points this year.
Grants are now only given to those students who achieve at least two A-Levels at grade C.
In GCSE English, 63.9% of entries got at least a grade C, compared with 65.4% last summer.
Just over a third got a grade C or above compared with the 74.2% getting the equivalent Intermediate GNVQ.
Ministers also said it was not acceptable that childcare professionals are not required to have at least GCSE grade C in English and maths.
The group says students were treated unfairly when exam boards raised the mark needed for a grade C between exams taken in January and June.
Mr Oates suggested scores could avoid some of the problems seen last summer, when many GCSE candidates failed to get a predicted grade C in English.
In 2011, just under two fifths - 38.9% - of FSM pupils who were taught at outstanding schools scored five GCSEs at grade C or higher, excluding equivalents.
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