Callum Hurley, from Peterborough, and Katy Moore, from London, claimed the government’s decision to allow fees to rise breached human rights and equality laws.
The 18-year-olds argued that the scale of the tuition fee increase – up from a maximum of £3,290 a year to £9,000 this year – was unlawful because it contradicted legislation, which sets out a right to education and a right to education without discrimination on any grounds.
Higher fees would discriminate against poorer students and those from ethnic minorities, they argued.
But High Court judges have rejected calls to quash the government’s policy.
They did say that the government had failed to comply fully with its public service equality regulations, but said it would "not be appropriate" to quash the regulations because there had been "very substantial compliance".
A spokesman for the Department for Business, Innovation and Skills said: "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."
Despite losing much of their battle, the students insisted the case had been useful in highlighting the government’s “rushed reforms”.
Katy Moore, who is taking her A-levels at Lambeth Academy in south-west London, said: ““I'm very pleased with the outcome.
“For the court to recognise the government’s actions as unlawful is a great achievement.
“It shows that it is possible to challenge decisions made by our government that have damaging effects on the future of our society, and win.”