But he did not have the speed to match Newgarden and Pagenaud, who finished one-two in the title standings, while New Zealand's Scott Dixon was third after his fifth placing.
There was a moment when Pagenaud thought he still might have a chance to repeat as series champion.
Simon Pagenaud did what he had to do to win IndyCar's season championship Sunday at Sonoma Raceway. In the scenario presented to him, he only needed to finish in the top three to achieve the season crown.
Dixon not only had to adjust to his team's return to Honda engines and aerodynamics kits, he was also robbed at gun-point after winning pole at the Indy 500 before crashing out of the prestigious race in frightening fashion.
Dixon just couldn't find a way past the other Penske cars to have a crack at Newgarden.
Post-race, the 37-year old Aucklander reflected on a challenging season.
Pagenaud emerged from his late final stop ahead of Newgarden, who couldn't find a way past, finishing 1.0986 behind Pagenaud - but 13 points ahead of him in the final season standings.
"I am looking forward to next season".
Somewhat content to sit behind teammate and eventual race victor Simon Pagenaud for the last 20 laps of the 85-lap race, Newgarden finished second in Sunday's Grand Prix of Sonoma at Sonoma Raceway to clinch the IndyCar series title.
The Kiwi slipped by Takuma Sato off the line but, as the race settled, found it tough get past one of his oldest rivals Castroneves.
Newgarden was able to close the gap when Pagenaud made a pit stop on the 65th lap, and Pagenaud was resigned to the inevitable. It paid off when he came out in front of Newgarden after his final stop. But it proved too late as Newgarden had a brief tussle with Pagenaud before eventually backing off to secure second-place and overall honours. And Helio was kind of a massive road block.
"Whenever we pitted short, they just pitted with us".
Newgarden said it was hard to go against his natural instincts and back off in the latter stages.
"It was so insane cool to do this", said Newgarden, who became the first American to win the overall title since 2012. I don't even know what to say - it was all year. I didn't make any stupid mistakes, didn't break a wing, didn't have any contact at any point. "I give a lot of credit to Tim to keep me in check". It was a full team effort today.
"It is a dream come true".