The FIA deemed that Hamilton had performed a practice start beyond the area specified in the pre-event notes issued to teams by race director Michael Masi.
The Briton was handed two five-second penalties.
After taking the penalty at his only pitstop, Hamilton finished third behind teammate Valtteri Bottas and Red Bull's Max Verstappen, and he also received two penalty points, putting him close to a potential race ban.
Wolff revealed that after the investigation was announced, shortly before the start of the race, he and Mercedes sporting director Ron Meadows went to see the stewards.
Wolff also insisted that he wouldn't apportion blame to Hamilton or the team for triggering what he called a "far-fetched" penalty.
"The errors always happen together," he said when asked about the incident by Motorsport.com. "It's not a team error, it's not a Lewis error. And I wouldn't want to point at anybody, and I've never done that.
"Ron [Meadows] and I were the stewards, the verdict was he wasn't in the right place. There is no mention what the right place is in the director's note, nor is it in the regulations. So we disagree on that one – we agree to disagree on that one.
"The other one was not driving at constant speed in the reconnaissance laps, and there again, it's debatable. But the race has happened.
"He received the 10 seconds penalty. So for a reconnaissance lap infringement an in-race penalty can be debated also. But you have to take it on the chin and move on.
"I'm not happy with the penalty, because it's far-fetched, but we agree to disagree. I will always respect the stewards in their job, but on that one, we just agree to disagree."
Wolff insisted that Masi's notes did not specify exactly where drivers could conduct practice starts, suggesting that Hamilton complied.
"The race director's notes say, if I'm well-informed, that you must do practice starts after the lights on the right side of the pitlane. And that's what happened.
"The designated place, it says after the lights, at the right side. It does specify that the practice starts need to be done after the lights on the right side."
Wolff insisted that Hamilton gained no advantage by doing the start where he did.
"You know, things are not always black and white, and there's room for interpretation. There are rules that can be interpreted in two ways. There is common sense.
"There is the fact that then that an in-race penalty was given, actually two in-race penalties were given, for an infringement that happened before the race.
"And there was an argument that he gained an advantage by making the [practice starts] there, I think it was not an advantage because there was no grip, so much less grip than you would have on your starting positions. It is what it is at the end of the day, obviously, we're all emotional about that.
"But the emotion should be geared towards Valtteri who deserved a race win since a long time, and that is fundamentally what makes me happy. And finishing once and three should give us all reason to make us cheer and fly home and say, we can be satisfied with how it went, and now we need to learn from the incident.
"We need to look at the procedures and our communications. And as every time we will not blame the person, we will target the problem."