McKenzie's injury was not considered serious and he could have played on Friday if the game had been a final, Cooper told reporters on Wednesday.
Leger primarily played as a midfield back for the Auckland Blues last season but with an abdominal strain to backup flyhalf Jack Debreczeni, Cooper said he had to give the 21-year-old an opportunity in the pivotal role.
"We don't want to risk either of them (McKenzie and Debreczeni) and Orbyn Leger went pretty well in pre-season, so he gets an opportunity," Cooper said, adding that he had to be mindful of the World Cup later in the year in terms of managing the players' workloads.
All of New Zealand's Super Rugby teams are required to give their All Blacks players at least two games off during the season in a bid to avoid burnout before the global showpiece starts in Japan in September.
Cooper said he was unsure if Friday's game would count as one of McKenzie's mandatory stand-down matches but did not want to take a risk with his ankle a World Cup year.
Cooper added he had been reluctant to throw Stephen Donald into the fray straight away.
The 35-year-old, who kicked the winning penalty in the All Blacks' 8-7 victory over France in the 2011 World Cup final, re-signed with the Chiefs earlier this week after Tiaan Falcon was ruled out for the season with a torn Achilles.
Donald last played for the Hamilton-based side two years ago and has more than 100 games for the team. He was named on the bench for Friday.
Atu Moli returns at loosehead prop for the side after he recovered from a serious quadriceps muscle injury last year that could have cost him his leg.
(Reporting by Greg Stutchbury; Editing by Peter Rutherford)
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