After Rovers had battled back to 1-1 in the 67th minute, Fijian midfielder Pita Rabo sealed the victory for the underdogs in the 86th minute when he got his head to a long ball from goalkeeper Matt Borren and nodded away from Rovers' custodian Shaun Peta to seal the victory.
Earlier, Vanuatu international and one-time ASB Premiership golden boot Seule Soromon had given United their 24th minute lead when he headed home a Dale Higham cross.
Napier's Fergus Neil made the most of some hesitant Wairarapa defending to score from close range to tie it up with 23 minutes to play.
But there was no denying Rabo and his Wairarapa teammates.
"It's a special feeling, said Rabo as he savoured what, at the start of the season, must have been a hopeful dream for a team eliminated at the first hurdle a year ago. "It is a special cup.
"Every player wants to score a goal in the Chatham Cup final but to score the winner is something special and I'm so glad that I could score in the last minutes."
A potential turning point came early in the second half when the pacey Higham got in behind the Napier defence and was brought down in the area by Danny Wilson.
Wairarapa skipper Adam Cowan stepped up to take the penalty but struck the crossbar to give Napier a lifeline and Neil scored soon after.
A jubilant and relieved Cowan said despite the setback, his side's belief had never wavered.
"We were very confident that we were going to get another goal at some stage," said Cowan. "Unfortunately I missed that penalty and they got an equaliser halfway through the second half.
"But as a unit we were confident that we could score another goal and that's the way it turned out with Pita Rabo stepping up."
Wairarapa United coach Phil Keinzley, who has brought the club up through the divisions in recent seasons, said the dream of winning the 89-year-old trophy gained momentum when they knocked over three-time winners Waitakere City 4-1 last month.
"At the start of the season winning the Chatham Cup was just a dream. It wasn't until we beat Waitakere in the quarter-finals we thought it could happen."
Scott Robson, who played a major part in their 1-0 semifinal win over Bay Olympic, was again a standout alongside Waisake Sabatu and James Oxtoby and picked up the Jack Batty Trophy for man of the match.