It came after players were forced off the field for nearly 45 minutes due to lightning.
The Waratahs trailed for the majority of the first half, with Moana Pasifika motivated to perform after a tough week saw their future in Super Rugby all but confirmed.
Isaac Kailea scored after the break to put the hosts in front, with Sid Harvey's second coming right before the delay.
Folau Fainga'a's last minute try wrapped up full points in an unconvincing performance that keeps them firmly in finals contention.
