Ellensohn timed his back post run perfectly to meet Cole Peverley's 38th minute free kick with a powerful header down and beyond Fabian Cerda for the game's only goal.
Chile won the first match on Wednesday 2-1, following a 4-3 win and a 1-1 draw in a two match series against Australia in Darwin.
Chile were reduced to nine men late in a tetchy second half, as tempers flared and referee Mat Conger was forced to flash red cards -- to complement a match total of 8 yellows -- to Bastain Arce (67th minute) and Esteban Paredes (89).
The win -- the first for a New Zealand side over Chile -- was a timely leaving present for Stu Jacobs' side a week before they depart on a five-match Olympic build-up tour of Australia and Indonesia on their way to Beijing.
"It's a hell of a coup," Jacobs said.
"Wins over South American sides aren't easy to come by, and it shows what this side are capable of.
"The more we play together, the better we'll get. This win will build character."
Ellensohn could've put New Zealand ahead after 15 minutes but his close range effort was kept out by Cerda, while Peverley should've made more of an unmarked header after 23 minutes.
In between, New Zealand goalkeeper Liam Little pulled off the save of the match in the 19th minute, reflexing away a Boris Sa Gredo header from point-blank range.
The game threatened to boilover just before halftime with a crunching tackle on Henderson followed by more flared tempers.
But Ellensohn remained lively throughout the match picking off passes from Chile's back four to set up dangerous counterattacks as New Zealand tried to extend their lead.
Tensions reached breaking point for Chile when an 89th minute penalty shout was turned down by Conger, and captain Esteban Peredes was given his marching orders for striking his marker at the ensuing corner.
New Zealand depart for Australia on July 10 for games against Australia's under-23 and the Central Coast Mariners, before travelling to Jakarta -- where they'll be joined by over-age players Simon Elliott and Chris Killen -- for games against the Indonesian National team and two club sides.
New Zealand face China (August 7th), Brazil (10th) and Belgium (13th) in group C of the Olympic football tournament with Blackburn Rovers captain Ryan Nelsen joining them for the first two games in Shenyang.
Result: New Zealand 1 (Daniel Ellensohn 38) Chile 0 (Halftime 1-0)
