The 24-year-old Phipps is originally from Sydney but moved south to the Rebels when they began playing in the Super Rugby competition in 2011.
"Nick has played a major part in laying the foundations of this club and it is disappointing to see him leave," Rebels coach Damien Hill said.
"We have identified and developed some great talent within Australian rugby, who are now coming off contract and the reality is, these players now attract interests from other clubs with different financial circumstances."
Phipps made his Test debut against Samoa in 2011 and has since earned 12 caps, including starting in eight out of the Wallabies last nine matches when Will Genia was sidelined with a serious knee injury.
"Nick is a good threatening, attacking player," Waratahs coach Michael Cheika said.
"He's good all round, in attack, in defence and with his kicking game; he's a quality player and I think that he's still got a lot of potential to fulfil."