In a video message to an awards ceremony held by a global network for Australian expats, Advance.org, Morrison said they had carried a "very heavy burden" over the past year and a half.
"I know for Australians overseas, it has been a very difficult and frustrating time," he said.
"It's tough, living through a pandemic, and being separated from your family, and that's brought its own heartbreak.
"Life's moments missed that you will never get back. Zoom can't do justice to these moments."
The government has faced sustained criticism from Australians unable to get home due to strict border rules and international flight caps, with 38,000 people registered at the end of July as wanting to return.
Morrison said the government had helped 53,000 Australians get back since the pandemic began, including on 167 facilitated flights.
"I also want you to know that these strong border controls though have been instrumental in saving over 30,000 lives here in Australia. Because on a per capita basis, that's the lives that would have been lost if our death rate was just the same as the average of OECD nations," he said.
"Your sacrifices have made that happen. You have saved lives by enduring and going through those difficulties.
"So thank you, I do appreciate it. And your fellow Australians do also."