Houston, who said in August a "yes" vote would have wide-reaching ramifications, has encouraged Australians to "move forward in unity and love, viewing one another without labels".
He said in the statement released on Wednesday: "I believe every person is created by God with a plan and purpose, and the focus of Hillsong Church has always been - and will always be - to point people to Jesus.
"As we move forward as a nation and put what has been at times a divisive debate behind us, my prayer is that we replace anger, criticism, hatred and intolerance with love, understanding, acceptance and kindness."
However, Houston maintained that his personal belief on the biblical definition of marriage will not change and urged the government to protect churches who do not agree with gay marriage.
He added: "The work of our church will continue as usual as it does in many parts of the world where same-sex marriage is legal.
"It is vital however, that legislation protects the rights of churches, pastors and others to hold contrary beliefs based on the traditional teachings of scripture.
"Freedom of religion is a fundamental part of a democratic society and must be upheld. Any attempt to force Christians to compromise their faith would be wrong."
He reminded Christians that "Jesus taught us that holding firm to our convictions, and respecting and appreciating other people who hold different views, are not mutually exclusive".