Trott left the Ashes tour immediately after Australia's crushing 381-run win in the first Test at Brisbane, with the England and Wales Cricket Board revealing he was struggling with a long-term condition.
Warner had previously told a press conference that Trott's second-innings dismissal in the match as "pretty poor and pretty weak" - something which raised hackles in the England camp given Trott's behind-the-scenes troubles.
Warner, addressing the issue for the first time, made some attempt to atone for any error of judgment in his comments but insisted he had no knowledge of Trott's off-field condition at the time.
Warner, who has been an unpopular figure with England ever since he aimed a punch at Joe Root in a nightclub last summer, told Fairfax Media: "We didn't know anything about an illness or what not.
"It's sad to see anyone go through that tough period and obviously if he's got an illness that's there we hope he gets the right people to help him out.
"We know the world-class kind of batter he is: he averages 50 in Test cricket and he has been a great player, a rock for England. I wish him all the best and I know our team wishes him all the best. I hope he gets well soon and [is back] playing the best cricket he can."
As for some of the opprobrium heaped on him following his assessment of Trott's performance at the Gabba, Warner offered a gesture of contrition.
"I was always going to cop criticism no matter what from what I said," he said.
"As I said before, I probably stepped over that line and at the end of the day it's cricket. We've got to go out there and play the best we can and as hard as we can without crossing that line.
"Going into public and saying what I did probably did go over the line a little bit. Obviously it's unfortunate that [Trott] has gone home now. I hope he gets well because we know the type of player he is and he will bounce back from it."
Australia captain Steve Waugh had earlier on Friday described Warner as "out of order" for singling out Trott during the Gabba Test.
Speaking to the Sydney Cricket Ground's official website, Waugh said: "I think Dave Warner's comments were out of order. I don't believe you should comment on someone else personally on the opposition.
"He can make a generic comment, but I think when you get personal like that, you cross the line on how players treat each other, and the respect they should have.
"So I didn't agree with Dave's comments. Having said that, he probably did smell a bit of fear in the England opposition players.
"Unfortunately for Jonathan Trott, it was a personal issue, and you don't want to keep going on about that. You just want him to get better and get well. So I think that hopefully has been put behind in that last Test match, and won't be brought up again."
There were other issues to arise at the Gabba, including Australia captain Michael Clarke being fined for a comment aimed at England's James Anderson which was picked up by the stump microphone.
It has brought the issue of sledging back to the table but Warner's comments aside, Waugh - who made 168 Test appearances in the Baggy Green - does not see too much of an issue.
"In the overall scheme of things I don't think there was that much controversy. I think I've seen Test matches like that played every week of the year," he added.
Australia have been keen to stress they will maintain their intensity both in terms of their play and their approach, but Waugh has encouraged them to reign it in a little.
"I think Australia probably need to be a little bit more clever about the way they're going about things. They're playing well, so they don't need to do so much talking out there now," the 48-year-old said.
Pace bowler Peter Siddle has indicated the chat will continue, though.
The Victorian was part of a three-man attack which terrorised England in Queensland and believes an aggressive approach is needed.
"It's a battle out on the field and we go about it how we think it will work," he said.
"We'll just keep playing hard cricket, we'll keep putting the pressure on them and keep going from there."
He also does not think Trott's situation should make his side check their behaviour.
"It's disappointing for him (Trott) to be going home, (we) wish him all the best, but we're going out there trying to win Test matches and however we do that, we'll play hard, aggressive cricket," he added.