The striker caused havoc for the Kiwi FC defence displaying his uncanny skills.
Despite being heavily marked Totori found the back of the net in the 32nd minute with a low strike past goalkeeper Masi Toetu.
The goal moved Totori's tally to 20, two ahead of Auckland City's Daniel Koprivcic.
Earlier Sam French scored the opener in the 19th minute. French tapped the ball from his right foot towards his left and then rifled the ball in.
Kiwi FC from Samoa tightened its defence in the second half denying Waitakere United a chance from extending their score.
Waitakere United coach Paul Temple said they wasted opportunities in the second spell.
Temple said Totori proved to be a threat to the opposition.
"We are pretty happy with the result," he said.
"We were little bit wasteful in the second half and missed our chances to score more goals. I think we will stick to what we have been doing as it worked in our system.
"In this competition there are less chances and you need to take them. It is good to have Benjamin in the team. He is always a threat and gives us something different."
Kiwi FC making its debut in the competition looked rattled in the first half after the two goals.
However the side with players from New Zealand, Solomon Islands, England and Japan regrouped at halftime and matched Waitakere United.
Kiwi FC coach Martin Tamasese said the side did not have much training time together.
Tamasese said Waitakere United was superior.
"We did not have enough time together but we were able to hold them in the second half," he said.
"Comparing our team from Samoa to New Zealand, it is a different level. But we played with passion. Our overseas players joined on Sunday and I'm happy with the overall performance."
Kiwi FC: Masi Toetu, Linton Dauara, Andrew Setefano, Jarell Sale, Barry Lewis, Michael Fifi'i, Mike Saofaiga, Lionel Taylor, Jamie Mason, Yuta Sahara, Jimmy Hoasihita.
Waitakere United: Danny Robinson, Aaron Jones, Brian Shelley, Tom Biss, Sam French, Benjamin Totori, Joel Stevens, Sam Mathews, Tristan Prattley, Jake Butler, Harshae Ranig.
LAUTOKA, (FIJI TIMES)