Lawyers for 17-year-olds Callum Hurley, from Peterborough, and Katy Moore, from Brixton, south London, argued that allowing universities to charge students up to £9,000 a year was unlawful.
Today Lord Justice Elias and Mr Justice King, sitting in London, ruled that Business Secretary Vince Cable had failed "fully to carry out" his public sector equality duties before implementing the regulations.
But the judges said it would "not be appropriate" to quash the regulations because there had been "very substantial compliance".
Katy is studying biology, chemistry, maths and history for her A-Levels at Lambeth Academy. She hopes to become a research scientist, exploring cells, diseases, new treatments and cures as a career.
Callum, from Orton Goldhay, Peterborough, attends Peterborough Regional College, where he is studying for a level 3 BTec in web development and wants to go to university to study IT.
It was argued on behalf of the teenagers that the fees increases would erect "a barrier" to higher education and threatened to widen the already large gap between rich and poor.
The judges were told that the case raised important equality issues, and the less well-off, the disabled and members of black minority ethnic groups would be particularly hit.
Tessa Gregory, of Public Interest Lawyers, which represented the teenagers, said they were "disappointed" that the court chose not to quash the regulations but pleased with the court's criticism of the Government's failure over its equality duties.
Ms Gregory said: "In its ruling the court made a clear declaration that the Government, when it passed the regulations increasing tuition fees, failed to comply with its public sector equality duties.
"It found the Government's analysis on equality issues was inadequate.
"That the court made this finding in relation to such a key plank of the Government's higher education policy cannot but reflect badly on these rushed reforms."
She added: "Whilst our clients, Callum Hurley and Katy Moore, are disappointed that the court chose not to quash the regulations, they are pleased with the recognition that the Government failed in its duties to properly think through the equality implications of its decision.
"The court accepted that some students would be discouraged from applying to higher education institutions because of increased fees but considered it too soon to tell whether the rise infees would discriminate against people from lower socio-economic groups.
"We continue to believe it will and intend to keep the emerging evidence of this under careful scrutiny.
"The Government has accepted that it must keep under review the impact of its measures and the court has stated that in doing so the Government must actively seek out evidence where none is available.
"Following the judgment, we will be pressing the Government to now perform its duties in a conscientious way and ensure that the impact of higher fees is properly and robustly analysed."
A spokesperson for the Department for Business, Innovation and Skills welcomed the court's decision, saying: "We are pleased the court rejected outright the suggestion that our student finance reforms breach students' human rights.
"The court recognised the consultation and analysis we carried out.
"It also recognised the extensive debate which took place, both inside and outside Parliament, on how those from disadvantaged backgrounds can be encouraged to enter higher education.
"Accordingly, the court has not agreed the claimants' request to quash the regulations, which set out tuition fee limits.
"This means that students and universities have the certainty to plan for the next academic year, and the Government's higher education policies remain the same."
PA
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