The hosts were penalised in what turned out to be the penultimate over of the innings which was declared at 557 for five in 169 overs.
Jadeja, facing pacer Trent Boult, ran straight down the middle of the pitch attracting a second warning from umpire Bruce Oxenford and with it a penalty of five runs for his team.
As a result of the penalty, New Zealand were awarded five runs even before the the start of their first innings.
Different penalties for bowlers and batsmen running on pitch?
"In countries where the wickets deteriorate like this, the umpires have to be very decisive around how they look after the middle of the wicket. There are rules in place and the need to stick to those," felt New Zealand coach Mike Hesson.