It was impossible to separate the sides after 90 minutes, as Napier dominated the second half but Suburbs always posed the most dangerous threat on the counter attack.
In a frantic game that switched from dull to thrilling after the halftime break, there were three moments of real quality that defined the match
Brandon Barnes, who was one of four UK recruits that helped Suburbs convincingly claim the Northern Premier League title with four games to spare, curled in a stunning 25-yard freekick to open the scoring shortly after the restart, and celebrated with 'the Hakerana' dance, made infamous last week by former English Rugby international Matt Dawson.
The strike kicked Napier's stuttering attack into action. They dominated the second spell and deservedly equalised when Central League Golden Boot winner Ryan Tinsley controlled with his chest before sending a swiftly hit right footed volley into the bottom corner.
With regulation time running down, both sides had glorious chances to win the match. Bryant, Bowen and Thomas Shaw all missed sitters for Surburbs while Miles John hit the bar for Napier and Saul Halpin may have a sleepless night after missing three clear-cut chances late in the match.
Suburbs, who were promoted to Auckland's top tier league this season have had a fairytale year and coach Malcolm McPherson's clever eye for recruiting played a big part.
Canadian striker Bowen and the English attacking midfield duo of Barnes and Bryant were potent in attack and had an air of authority around the box.
Suburbs were stretched at times in midfield and lost some fluidity as the match wore on but they always presented a serious attacking threat and their late winner highlighted the importance of keeping composure in the box. They also looked like a team who were used to winning. After putting together an incredible 19-game win streak this season, McPherson said the squad had developed a powerful aura of self-belief.
"We've got some talent in the group but as you saw today we've also got so much fight and grit,: said McPherson. "When you need to churn out a result, which we've had to do so many times this season, our players have consistently stood up.
"You can have as much defensive shape as you like and keep the opposition at bay as much as you like but if you don't have players that can change the game you are going to struggle. And we are fortunate enough to have two or three this year."
Suburbs are the first team to do the League and Cup double since Central United in 2002.
In the Women's Knockout Cup Final Glenfield Rovers beat Massey University 4-0.
Eastern Suburbs 2 (Brandon Barnes, Damien Mosquera)
Napier City Rovers 1 ( Ryan Tinsley)
HT 0-0
1-1 after 90 mins.