The move comes after the parties failed to reach a settlement at a conciliation hearing at the end of June.
Folau's unfair dismissal case was launched after he was sacked by Rugby Australia in May for posting anti-gay messages on social media.
The 30-year-old rugby star is a Christian and argues his contract termination was an unlawful act of religious discrimination.
"I confirm I have commenced court proceedings against Rugby Australia and NSW Waratahs," Folau posted on his personal Twitter account, alongside the message 'God Gives Me Strength For The Road Ahead'.
"Thank you to those who have supported me over this journey - it has meant so much to (wife) Maria and me. God bless."
Neither Rugby Australia nor the Waratahs have made any response to Folau's statement that he has launched legal proceedings against them.
Folau has been fundraising to help cover the costs of his legal action.
Over two million Australian dollars (£1.1million) has been raised after the Australian Christian Lobby set up a fundraising page.
The ACL effort replaced an earlier campaign on GoFundMe, which was taken down by the platform for breaching its service guidelines.