Edinburgh University was ranked first in Scotland and 36th in the world after climbing four places in the Times Higher Education World University Rankings 2011/12.
St Andrews University came second in Scotland with a ranking of 85th in the world, compared to 103rd last year -- the first time it had been out of the top 100 since 2006.
Glasgow University came third in Scotland at 102nd, compared to 128th last year, while Aberdeen came 151st and Dundee 176th.
Scottish universities are likely to see the rankings as evidence their courses are worth the fees that have been introduced for students from the rest of the UK.
Alastair Sim, director of Universities Scotland, which represents university principals, said: “These rankings show once again Scotland’s universities continue to punch above their weight on the global stage. For a country Scotland’s size, this is a remarkable achievement.
“Scotland’s universities can only continue to compete with the best in the world if we are confident of sustainable investment.
“The Scottish Government’s spending review settlement for universities as announced recently is vital to this going forward as it puts us on a competitive footing for the future. We strongly welcome that investment in Scotland’s success.”
A spokesman for Edinburgh University said: “Any rise in a league table position is always to be welcomed.”
Louise Richardson, principal of St Andrews, also welcomed the rankings. “We are very pleased St Andrews has been placed in the top 100 universities in the world. It is gratifying to be rewarded for our strengths in research and teaching in the world’s largest academic reputation survey,” she said.
A spokesman for Glasgow University said: “These rankings show Glasgow has, once again, performed remarkably well. Taken with other surveys, this confirms Glasgow’s position as one of the world’s leading universities.”
Overall, three UK universities were ranked among the top 10 in the world, with Oxford leading the way.
The latest world university rankings revealed the UK still has the second-best education system worldwide, although the authors raised concerns funding cuts and higher tuition fees could damage its standing.
Oxford was rated the UK’s best university, coming fourth in the new table. It was above Cambridge, which was sixth.
The US dominates the table again, with 75 institutions in the top 200. The California Institute of Technology topped the table, followed by Harvard University and Stanford University in joint second place.
Only the US and the UK had universities in the top 10.
Ann Mroz, editor of The Times Higher Education magazine, said: “The UK is blessed with some truly brilliant universities, more brilliant than the Government understands judging by its hastily concocted higher education reforms, with all the uncertainty they entail.
“While we may be second to the US in terms of the overall number of world-class institutions, given the disparity in funding levels our performance is nothing short of staggering. Put simply: we spend much less on our universities than many of our competitors, less than the Organisation for Economic Co-operation and Development average and yet outperform almost all of them.
“These facts make the massive gamble we are now taking, by all-but-abolishing public funding for university teaching and replacing it with tuition fees, all the more questionable. The Government should heed these ranking results, reflect on concerns raised and think again.”