It marked McLaughlin's second straight win in Alabama. He beat teammate Will Power of Australia by 1.3194 seconds after leading 58 of 90 laps around Barber Motorsports Park in Birmingham on Sunday.
Their 1-2 showing came after Team Penske received sanctions for illegal use of the push-to-pass system in the season opener at St Petersburg.
Josef Newgarden's win there was vacated as he and McLaughlin were disqualified from the race, while Power was docked 10 points.
"It's definitely one of my best drives in terms of just execution and just knocking out the laps," McLaughlin said.
"Really happy we could advance to the checkered flag there and bring home a 'W' for Team Penske and for Roger."
Fellow New Zealanders Marcus Armstrong was 9th and Scott Dixon 15th.
McLaughlin said he and his teammates did not necessarily come to Barber feeling they had something to prove.
"No, we just gotta keep rolling. We know our job. We know what we need to do. I was just so proud of our execution."
McLaughlin led Spaniard Alex Palou by nearly 30 seconds ahead of his third and final pit stop, enough cushion to keep a narrow lead when he came off pit road. But a late caution meant McLaughlin and Power had to duke it out in a two-lap sprint.
"It was a hard-fought 1-2 for Penske," Power said. "We were certainly fast, but obviously a lot of strategy played into that. We were able to use our speed to come out in front again."
The win pushed McLaughlin into ninth in the drivers' standings, while Power is now one point behind series leader Colton Herta, who came home in eighth.
IndyCar rookie Linus Lundqvist of Sweden earned his first podium finish, taking third place for Chip Ganassi Racing.
- Field Level Media