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Leinster scored four tries in the second period, with Fergus McFadden's double helping them to a 30-23 triumph after Luke McGrath and van der Flier had already crossed the whitewash.
However, the Leinstermen - statistically the Guinness PRO12's tightest defence - were never out of sight with Tom Brown, Mike Allan, and Sean Kennedy all going over for Edinburgh to earn the visitors a losing bonus.
And Ireland flanker van der Flier admitted his side, who are top of the PRO12 with two rounds to go, had to take the win with a pinch of salt as a result.
"Edinburgh are a fantastic team," said the 22-year-old. "They really kept coming at us, even when our attack was going well in the second half.
"I was delighted, obviously, to score. But it's all about the team getting the win, which is what we wanted.
"We can't be conceding tries that easily, as good as Edinburgh are. That was probably disappointing.
"Definitely we said inside there after the game that that's something we really need to work on. Our standards have to be higher than that.
"Every game is like a final from now on, really, with how tight the table is. All we can do is focus on Ulster in two weeks and try to get the win there."
Head coach Leo Cullen echoed van der Flier's sentiments, conceding the frantic second half had been a real mixed bag for his side.
He said: "Edinburgh went hard at our ball. It was a frustrating first half - we played into a very strong breeze.
"In the second half, I think it was important that we kept on with that same intent. I thought we looked quite sharp in attack, created some more good chances.
"We took them. We were a bit more clinical, I thought, in the in the second half. The game got a little bit loose after that.
"It's disappointing - the fact that we gave up three tries - because our defence has been very solid all season.
"But if you'd offered up five points up at the start of the day, we would have been very happy with that."
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