The case against Harry Nicolaides, who was arrested in August, was the latest in a slew of lese-majeste investigations in Thailand that rights groups say stifle freedom of speech and political dissent.
In brief comments to waiting media, Nicolaides said he had only a few hours notice of his release.
Upon boarding the flight in Thailand he was told his mother Despina had been admitted to hospital after suffering a stroke. Asked how he felt, he said: "Bewildered and dazed, nauseous. I have been crying for eight hours."
Nicolaides, 41, said that when informed of his release he was asked to kneel before a portrait of Thailand's King Bhumibol Adulyadej, which he described as "a royal audience of sorts".
"I ran out of tears but I never ran out of hope or love," he added.
A spokesman for Australia's foreign ministry said Canberra appreciated the "expeditious handling of the pardon" by the Thai authorities.
Lese-majeste, or insulting the monarchy, is a very serious offence in Thailand, where many people regard the 81-year-old king as semi-divine.
It is punishable by up to 15 years in prison although convictions, especially of foreigners, are rare and are normally followed quickly by a pardon.
Nicolaides' offending novel 'Verisimilitude' was published in 2005, but at the time of his arrest only a handful of copies had been sold.
A Swiss man, Roland Jufer, was sentenced to 10 years' jail in 2007 for spraying black paint on pictures of the king but was pardoned at Thai New Year in mid-April after serving only four months. Jufer was deported as soon as he was released.
Critics have questioned why a country that proclaims such devotion to its monarch needs such strong laws to protect his image. The Democrat Party-led government that came to power in December last year has vowed to toughen the laws yet further and blocked thousands of websites carrying anti-royal commentary.
A prominent Thai leftist academic, who was charged with lese majeste for comments made in a 2007 book about the previous year's military coup, said he could not get a fair trial in Thailand and fled to London earlier this month.
Critics and freedom of speech advocates say the government's crusade to protect the crown in the twilight years of King Bhumibol's six-decade reign is a pretext to crush political dissent and opposition.
Nearly three years after the coup that ousted former Prime Minister Thaksin Shinawatra, Thailand remains locked in a political crisis which has distracted policymakers from dealing with an economy on the brink of recession.
Analysts say the outlook for political stability remains bleak as long as the rift between Bangkok's royalist military and business elite, who accuse Thaksin of corruption, and rural voters who loved his populist policies, remains unresolved.