Along with veteran Bruno Alves, Pepe has been key in Portugal's style which has long relied on a solid defensive set up that allows Ronaldo the freedom to thrive in the attack.
Ronaldo was the one to break the deadlock, dispatching an emphatic penalty beyond Stefan Marinovic to score on the 30th birthday of nemesis Lionel Messi. "We know we've played some really good football at times".
"We managed to show good football", Russian Federation coach Stanislav Cherchesov said.
Portugal's all-time leading scorer swept the ball home in the 33rd minute, his 75th goal for his country, and Bernardo Silva added the second four minutes later.
His sharp headers could have turned a comfortable win into a rout.
With Ronaldo dominating All Whites defenders in the air midway through the first half, the next aerial challenge saw two leave him in a heap with rugby-style physical skills. Porto midfielder Herrera fired in a deep cross to the far post where Araujo lifted the ball over Akinfeev and into the opposite corner.
The hosts then upped the pressure midway through the second half and they nearly took the lead when a fantastic drilled shot from Fyodor Smolov hit the post with the goalkeeper beaten. Substitute Nani shot low past Marinovic in stoppage time.
New Zealand stuck to their task and did not let the quick-fire double deflate them, despite knowing they were staring at their third defeat from three games at the tournament and their 11th in 12 games played at Confederations Cup tournaments.
However, it was the minnows who created the first clear-cut opportunity of the match with Leeds United forward Chris Wood forcing a decent save out of Rui Patricio, who got down well to his left.
Even so, coach Anthony Hudson was proud of his side, who refused to shut up shop in the second half.
"I warned my players to not let them win balls in the air, and the team reacted well".
Portugal coach Fernando Santos said the scoreline didn't reflect the intensity of the match and felt New Zealand deserved a goal.
Russian Federation fought valiantly in Kazan but the hosts could not avoid early elimination from the Confederations Cup, losing 2-1 to Mexico, who join the Group A winners, Portugal, in the semi-finals after the European champions beat last-place New Zealand 4-0 in St Petersburg.
Mexico winger Hirving Lozano took advantage of an terrible mix-up in the Russian defence to score an extraordinary goal which gave his side a 2-1 win and knocked the Confederations Cup hosts out of the tournament on Saturday.
Luis Nani and AC Milan's new boy Andre Silva scored late in the game to seal the victory for Portugal and ensure they finished top on the Group A table.
Portugal topped Group A and joined the Mexicans after beating last-place New Zealand in St. Petersburg.
The News Agency of Nigeria (NAN) reports that Ronaldo emerged man of the match played at Saint Petersburg Stadium, St Petersburg (RUS) on Saturday.