Berry had been there for the deflection in the first half that the Athletic goalkeeper could not control in a own-goal moment, then got the first of his actual brace of goals with a patient and well taken right-to-left strike, after good lead-up work from Jack Jonas and Joshua Rod.
Athletic's reply goal came from Flynn Johnson making a find strike on a rebound out of goal, after pressure from veteran Scott Burney, who had dropped down from the 1sts for the match.
Towering defender Jack Donaldson, an aggressive Jonas, Berry and Max Davidson looked to impose themselves through the midfield, and consequently were the recipients of the yellow cards as well as the longest chats with the referee, while Athletic's Ryan Donaldson got one for his slide tackle, which felt like a ruling to maintain consistency.
Athletic player-coach Adam Tipper said his young side's defensive shape was alright, which was helped by veteran Anthony Floyd at the back, but they put too much pressure on themselves by staying there.
City had players with plenty of derby experience and they brought the energy to proceedings, leaving his side too reactive instead of proactive.
"Just sloppy mistakes cost us, first half especially. First time balls going astray," said Tipper.
Nonetheless, they will be better for the experience when the teams meet again in the second round of matches.
"Going forward, I think it's looking promising."
His opposite Kelvin Francis had much the mindset, saying they were a little surprised as City had expected an intense opening 10 minutes, but instead found the men in red sitting off them.
He still felt his side gave the ball away too much, going for 80-20 kicks when putting it forward through the feet would have done, along with needing to be a little more cautious as the yellow cards began to stack up.
"Just said to Jack [Jonas] at halftime, 'we need to simmer'.
"It just started to click for us later on.
"It's a young group of players, I coached both [sides players] in representative football, nice to see them out playing for their clubs.
"It's still early days and got to keep working."
City began getting shots on goal early through Jonas and Kyle Graham-Luke, while Athletic would have to wait until the 25th minute before they made Athletic's goalie have some work to do in front of his line.
It was like a game of human chess in the opening exchanges as City probed for openings, and although Athletic would get the turnovers, they worked their way back out of their half very cautiously, seemingly more concerned with accuracy than speed into gaps.
City gave them plenty of chances with free kick penalties after some more physical tackles, but soon had the ball back in their possession, missing out on a couple of cross kicks into the box before pressure from Rod and Berry led to the opening goal at 19 minutes.
There was no luck required in City's second goal after 25 minutes, as they rapidly counterattacked after Zeb Small created some rare Athletic chances, with Jonas forcing the turnover and feeding Rod, who gave Berry plenty of time to set and strike from long range.
The yellow cards and discussions continued for City, and coming into the second half Athletic were making better use of their possession, working forward in phases.
Burney managed to get a shot away and although it rebounded back from the defenders, Johnston was there to fire it home.
Athletic's surge of excitment was short lived, as Bell began to lift his game, making some end-to-end runs to set up corner kicks, before getting free outside the defenders and smoking home a 'don't argue' strike with the dreaded index finger on the lips after 75 minutes.
Berry then wrapped up proceedings inside the final ten minutes after Graham-Luke's cross was battered out of goal but the skipper was there to fire it back in.
The win moved City to the top of the table, after Palmerston North Boys High 1st XI lost their unbeaten tag 3-1 to Breakers RSM Reserves.
