Edinburgh University was ranked first in Scotland and 39th in the world after dropping seven places in the Times Higher Education World University Rankings 2013/14.
St Andrews University came joint second in Scotland alongside Glasgow University, with a ranking of 117th in the world. However, while St Andrews dropped nine places since last year's table, Glasgow has risen 22 places.
Aberdeen came 188th in this year's table after a fall of 12 places and Dundee was the fifth Scottish institution to feature, coming 196th in the world. Last year, Dundee dropped out of the top 200.
Universities Scotland, which represents university principals, said the figures showed the strength of Scottish higher education.
Alastair Sim, the organisation's director, said: "Everyone in Scotland can celebrate the fact we have more universities in the world's top 200 per head of population than any other nation, making us one of the strongest higher education systems in the world.
"Every Scottish institution is engaged in world-leading research, uses innovative learning and teaching methods, and looks to make a strong contribution locally, nationally and internationally.
"The continued success of our universities - in a fiercely competitive international higher education marketplace - is crucial to Scotland's success."
Education Secretary Michael Russell welcomed the figures, which he used to highlight continuing government investment in the sector.
He said: "Scottish universities are known at home and abroad for their excellence and this is highlighted by the fact that five of our universities feature in these international rankings."
A spokesman for Glasgow University added: "This confirms the reputation of Glasgow as a world-leading, research-intensive university where the student experience is second to none."
Overall, the rankings show the UK is holding its position, with 31 institutions in the top 200, more than any other country except the United States. The UK has three universities in the top 10, with Oxford taking second place alongside Harvard in the US. Cambridge University was seventh, and Imperial College London, tenth.
Top of this year's rankings was the California Institute of Technology, which was in first place for the third year running.
However, Phil Baty, the editor of the rankings, said leading UK universities such as Edinburgh, St Andrews and Aberdeen, as well as Manchester, Bristol and Newcastle, were at risk of losing their global reputations because many had slipped down the table.
And he suggested the "golden triangle" of Oxford, Cambridge and London was becoming the UK's last bastion of world-class education and research.
Mr Baty said: "On the whole, the UK has had a very stable year, with little overall change to its position behind the US as the world's second-best higher education nation. This is good news after stark evidence of decline in last year's rankings.
"But there are still concerns for our world-leading institutions … which have fallen to varying degrees. Although other institutions have risen, and some significantly, such global brands act as flagships for the rest of the UK, so this is a worry."
The rankings rate universities worldwide on 13 measures including teaching, research and their international outlook, which includes the number of overseas students and staff they have.