The 37-year-old Haddin asked to be stood down for the second test at Lord's because his daughter was sick and was not recalled for the match at Edgbaston for which understudy Peter Nevill retained his place.
Former Australia opener Matthew Hayden labelled Haddin's axing as 'outrageous' but Lehmann said the decision was taken because the wicketkeeper was out of form with the bat.
"Let's make it perfectly clear. Brad has been a fantastic cricketer for Australia for a long period of time and that would be the hardest decision I have had to make as a coach, or even as a player," Lehmann told reporters after England won by eight wickets on Friday to take a 2-1 series lead.
"I know there has been a very unbalanced view from a lot of people. We certainly care about Brad and his family. We had to make a decision on what we thought was the best 11 for this particular game."
Haddin had a poor game in the first test in Cardiff, scoring 29 in two innings and dropping centurion Joe Root before he had scored on the first morning when England had lost three wickets with only 43 on the board.
Australia handed Nevill a test debut at Lord's and he made a good impression with seven catches and a knock of 45.
He also kept tidily at Edgbaston and scored a patient 59 in the second innings -- occupying the crease for 147 balls, the most of any batsman in the match.
"The cold hard facts were that he's (Haddin) played the last 12 test matches, made 250 runs at 15, 16 (average). It gets down to performance. I know there has been a big hoo ha about family first," Lehmann added.
"Pete did a good job at Lord's. Very hard to change that side and did a really good job in this game.
"A really tough decision to make and one that everyone's going to have different emotions with it. That's part of professional sport."
Lehmann said Haddin had been "fantastic" in accepting being left out.
"I can't speak highly enough of how good he's been with Pete," he said.
"He's taken over the wicketkeeper coaching role as well as trying to do his own stuff to keep ready... one of the best blokes I've ever coached."
(Editing by Sudipto Ganguly)
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