Although some couples wed last month after obtaining special exemptions, most could not marry until Tuesday.
Australian athletes Luke Sullivan, 23, and Craig Burns, 29, exchanged vows and a kiss just after midnight in a small ceremony in New South Wales.
The beaming pair celebrated with fireworks.
Mr Sullivan said he had been overwhelmed with messages of support.
“My Instagram direct messages have blown up with people I have never met – I don’t know who [they] are – just sending love and congratulations, it’s really touching,” he told the Australian Broadcasting Corp.
The athlete married his partner, a sprinter who competed in the Glasgow Commonwealth Games, in front of about 50 family and friends.
“Equality where we can get married is a huge step forward for Australia,” Mr Sullivan said.
In Melbourne, Diana and Deanne Ribeiro wed a minute after midnight, in the same place where they held a commitment ceremony five years ago.
“It was just magical,” Diana Ribeiro told the Special Broadcasting Service.
The Australian parliament made same-sex marriage legal last month, following a national survey that showed support from 61% of voters.
A one-month registration period was waived for some couples with special circumstances, meaning they could wed before Tuesday.
Australia now joins more than 20 other nations in allowing same-sex weddings.
One local bank, ANZ, predicted that same-sex unions could inject A$650m (£375m, $510m) into the local economy in 2018. (Courtesy BBC)