The running was all with Souths, as Sam Burgess, in his comeback from a neck injury, and brother George, led the way.
But with Daly Cherry-Evans sidelined, Manly's makeshift halves combination of Dylan Walker and Apisai Koroisau then made their impact felt on the contest.
Against their old club Walker and Koroisau continually threatened the line with ball in hand as the locals began to dominate the forward battle.
Koroisau was rewarded for his hard work when he forced his way over on the hour mark as Manly bridged the score to 16-12.
The Sea Eagles enjoyed the best of field position for the final 20 minutes but couldn't land the killer blow as Souths bounced back well from their 42-12 thrashing to Canterbury last week.
Souths coach Michael Maguire was impressed with the way his side defended in the second half.
"We defended there for a long period of the game," he said.
"We put a bit of pressure on ourselves and we had a few calls go against us.
"But I am proud of the spirit we showed and the way we hung in there."
Manly mentor Trent Barrett said he was disappointed the Sea Eagles couldn't "ice" the game in the dying stages but wasn't upset with his players.
"That was our third game in 10 days. I was worried we might be flat early and we were. The start cost us," he said.
"But I couldn't go in there (the dressing room) and be upset with those guys, it was an unbelievable effort.
"We are coming together as a team. I can see that."
Prop Jake Trbojevic was a late withdrawal due to a knee injury but Barrett said he should be right for the trip to Auckland to meet the Warriors next week.
Barrett said he would stick with man of the match Koroisau and Walker in the halves until Cherry-Evans returns in a month's time.
"Api was great for us. He is a real tough kid and Dylan had some really good touches," he said.
- AAP
