On the back of 59 per cent of possession, the home side dominated the first half. Souths halfback Adam Reynolds opened the scoring with a penalty goal in the fifth minute but, after that, the Rabbitohs didn't trouble the scorer.
Jake Trbojevic crossed first for Manly in the eighth minute, when he charged onto a Feleti Mateo pass and crashed over. Hiku added his first eight minutes later when a trademark Brett Stewart long ball found him unmarked for a 10-2 scoreline.
Manly continued to enjoy the better of the exchanges in and around the ruck, with Souths committing a number of handling errors in their own half to stifle any momentum they might have gained.
Some stubborn defence from Souths kept the Sea Eagles at bay until Hiku scored his second from a lovely Jamie Lyon pass late in the first half. Two missed conversions from Lyon meant a halftime lead of 14-2 for Manly.
Things continued in a similar fashion after the break with Manly enjoying the better of the yardage up front and out wide. Hiku's third try put Manly out to 22-2 with 18 minutes to go, before Trbojevic's second in the 74th minute sealed the win.
Former Sea Eagle Glenn Stewart was put on report for an early second-half high shot on Manly's Steve Matai.
Kyle Turner was a late withdrawal for Souths after his concussion last weekend.
Jamie Lyon became the third Manly player to score 500 points at Brookvale after Graham Eadie and Matthew Ridge.
Manly coach Geoff Toovey said the confidence at Brookvale was growing.
"Our combinations are coming together and, if we can win a few more, we might sneak in (to the finals)," he said.
"I thought our forwards were great tonight, they controlled the ruck and there was skilful play from our backs.
"I thought Peta Hiku was outstanding. And there's not too many times you see a front-rower scoring the first and last try - Jake Trbojevic is pretty happy with himself."
Souths coach Michael Maguire said his side failed to find any rhythm throughout the game.
"We just didn't give ourselves an opportunity with the possession we gave them in the first half and that continued in the second half," he said.
"We got taught a few lessons tonight about possession and how to control the ball.
"I thought we turned the corner the last few weeks but tonight was a kick in the guts."
- AAP