It looked like Hendry was on track for a comfortable win before Lee kicked into gear to stir memories of the battle the pair shared for the 2010 Muriwai Open.
Lee, who began the day six shots back, rallied with five birdies in a row after the turn to put the heat on Hendry but the two-time NZ PGA champion was good enough to hold on.
Hendry's fourth Charles Tour victory draws him level with Doug Holloway as the most successful player on the local tour since it began in 2004.
"I am very happy to win my fourth Charles Tour title," Hendry said.
"It is nice to be leading little stats like that. If you can keep putting yourself ahead in the record books then it continues to put your name forward among the best New Zealand golfers."
Meanwhile, New Zealand representative Mun Chin Keh won the women's field after delivering a delightful chip-in on the par four 16th at the Muriwai Beach Links.
At that stage, overnight leader Jenna Hunter was in a share of the lead and in the middle of the fairway. Keh's chip-in appeared to rattle Hunter and she went on to four-putt the 16th and make a costly double bogey.