The seven-times Formula One world champion finished eighth and Leclerc ninth in the race in Baku.
Hamilton, who started 12th, said he got the message late on when he was still focused on trying to catch McLaren's Lando Norris.
"Basically I did lift on the straight, and did actually brake, but he (Leclerc) missed it by like four tenths," he explained.
"That was just a misjudgement by myself. I'll apologise to Charles."
Team boss Fred Vasseur said Hamilton appeared to have misjudged the position of the start/finish line and Leclerc indicated he was not too fussed.
"Honestly, for a P8 or a P9 it's not going to be a big talking point. I don't really mind," said the Monegasque.
"These are things that we agree between us and the general rules of how we want to work whenever there's a swap, it didn't happen and that's OK. It's not like I would have been a lot happier being P8."
[Source: Reuters]