She will succeed Western Sydney University Vice-Chancellor Professor Barney Glover in the role from May 16.
Professor Glover welcomed the election of his deputy as the next chair of the organisation.
“Margaret is an outstanding leader who has contributed impressively to the sector in a brilliant career,” he said.
“She’ll bring deep insight and formidable intellect to this role. The organisation will be in great hands.”
Professor Gardner thanked Professor Glover for his inspired and energetic leadership as chair since 2015.
“Barney has led the organisation wisely and well,” she said.
“Under his leadership, UA has delivered a significant number of major achievements.
“These included developing our major policy statement – Keep It Clever – ahead of the 2016 election, and our public awareness campaign about how universities generate future prosperity.”
“UA has also championed equity and diversity, launched the Respect. Now. Always. campaign to prevent sexual assault and worked with universities to make gains in Indigenous participation.”
Professor Gardner said she was honoured to lead the nation’s universities at a time when they were more important than ever to Australia’s economic and social prosperity.
“Universities play a crucial role in our community and economy as engines for ideas and growth,” she said.
“Great quality education and research enable us to solve intractable challenges, grow our economy, create new jobs and investment, and help Australian communities to be healthier, safer, and more secure.”
“They’re also at the heart of Australia’s openness to the world.”
“The internationalisation of our universities over the past three decades has positioned Australia very well.”
“The record numbers of international students we now see in our universities – who bring more than $21.8 billion in income for Australia each year – and the scale of our global research collaborations is crucial in this global century.”
“For brilliant scholars and researchers the world over, Australia now has enormous appeal as the place where they can build their careers and make their home.”
“And that’s a foundation on which we build the trade, diplomatic and cultural relationships to secure Australia’s future.”
Professor Gardner has been Vice-Chancellor at Monash since 2014, and is a former Vice-Chancellor of RMIT.
She has also held senior roles at the University of Queensland and Griffith University.
Professor Gardner is Deputy Chair of Universities Australia and a Director of the Group of Eight Universities.
In 2007, she was made an Officer of the Order of Australia (AO) for her service to tertiary education.