Whitelock injured his AC joint in his shoulder and is liable to be out for four weeks.
He left the field near the end of the first half in the match in Sydney, in what was a game of two halves.
The Highlanders showed some real spark on attack in the first half and were up 33-18 at halftime.
The Waratahs came roaring back and led 47-40 with five minutes left.Highlanders midfield back Rob Thompson then scored and when Fletcher Smith converted the game was tied up. Then Smith slotted a penalty to win the game 50-47 at the end.
Brown said the side looked polished in the first half.
"Our execution was spot on and we scored some good tries. Put them under pressure and took the chances that came along," Brown said.
"We made a few changes at halftime and we still did some good things in the second half and played some really good footy. But we lost a little bit of ball and when you do that against good teams you pay for it."
Brown said the team may have gone a bit individual in the second half but had come back well.
There was plenty to like about the first half.
The All Blacks were outstanding, with Ben Smith helping himself to two tries and Brown said winger Tevita Li and Thompson also played well.
The coach said Whitelock’s injury was disappointing but the side had back-up with All Black loose forwards Liam Squire and Elliot Dixon.
Utility back Richard Buckman and lock Joe Wheeler, who played in Japan over the off-season, including playoffs, did not turn out on Thursday night.
Brown said the duo would get some solid training into their bodies and would be unleashed in round two or three.
The side was based in Sydney all week, had a recovery session on the beach yesterday and was scheduled to be back in Dunedin late last night.
Reviewing the pre-season, Brown had a mixed response.
"I’m never happy but considering all the circumstances we are in as good as position as we can be."
The competition starts for the Highlanders on Friday night against the Chiefs at Forsyth Barr Stadium.
Brown has tweaked the side’s training week this season.
There would be more training and work at the start of the week and the side would have a day off two days before the match and then a short captain’s run on the day before the game.
Research had shown players responded to the lighter load nearer the playing of games but if it did not work out it may be changed.
Traditionally players had a day off midweek and then a solid training day, two days out from the match.