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Owen Farrell got away with a controversial tackle on Andre Esterhuizen beyond the 80th minute in a 12-11 victory over South Africa last weekend, but Eddie Jones's side saw a marginal call go against it on this occasion as Sam Underhill's 75th-minute try was controversially chalked off by TMO Marius Jonker.
Courtney Lawes was adjudged offside when he charged down TJ Perenara's kick before Underhill, who started at openside flanker in place of the injured Tom Curry, beat Beauden Barrett to score in the corner.
England went behind despite an electric start that saw Chris Ashton take less than two minutes to mark his first England start in over four years with a try and Dylan Hartley also cross to put the fired-up host 15-0 up.
Full-back Damian McKenzie finished a lovely move in the 39th minute to start the New Zealand comeback, before Barrett added the extras and finished the first half with a penalty.
A drop goal and another penalty from Barrett then put the All Blacks in front for the first time, and they held on after Underhill's late score was ruled out in debatable fashion.