ANU moved up two spots to be ranked 24th in the world in 2012.
The University of Melbourne came in 36th, down five places from its ranking a year ago.
Also making the top 100 were University of Sydney (39th), University of Queensland (46th), University of New South Wales (52nd), Monash University (61st) and University of Western Australia (79th).
The University of Adelaide came in at 102 and Newcastle University at 126.
Danny Byrne, editor of TopUniversities.com which complies the rankings, said Australia continued to punch above its weight, with the tally of seven institutions among the world's top 100 beaten only by the US and the UK.
But he said Australian universities were "feeling the squeeze".
"Although its top institution Australia National University rises to 24th, Melbourne drops five places to 36," he said in a statement.
"While Australian universities outside of the research-intensive Group of Eight have suffered a general decline in year-on-year performance."
ANU deputy vice-chancellor Margaret Harding said the result, along with last month's news the university rose six places in the Academic Ranking of World Universities, were a testament to the institution's high-quality research and teaching.
She was pleased to see Australian universities representing the country well.
"The results are a cause for pride across the whole university community, and a direct endorsement of the work and commitment of all ANU staff," she said in a statement.
The QS rankings are based on academic reputation, employer reputation, staff-student ratios, citations per faculty, international faculty and international students.
They take into account responses from 46,000 academics and 25,000 employers around the world.