The Owls played a back three for the first time this season but abandoned it at the break when centre-back Lewis Gibson and holding midfielder Sam Hutchinson went off injured. Gibson, on loan from Everton, was making his first League One appearance for the club.
The hosts reverted back to three central defenders once Lee Gregory scored the only goal of the game, converting a wonderful Jack Hunt cross.
"The objective this week was to win the cup match on Tuesday night (against Mansfield Town in the Football League Trophy) and get three points here today so credit to the players, it was a massive tick," said Moore. "I'm really pleased.
"We went for a different system today (3-4-1-2) and we had 48 hours to work on it so I'm really pleased with it."
Asked about the scratchiness of the performance, he replied: "I don't worry about the performance because we had 48 hours to work and my trained eye saw things I liked.
"When you consider what happened at half-time with two of your major players coming off, two major players in terms of the system, that's what disappointed me. They're big players for us.
"There are mixed emotions, not because of the performance, but losing those two players.
"It's too early to say the prognosis on those two so we'll have to see how they shape up.
"I'm not sure if they're muscle injuries, I'll have to have a look on Monday.
"To lose those two at the time disrupted the gameplan. We had more attacking players on the bench and as the game wears on, we would have liked to bring them on but I wasn't really able to."
Bolton came into the game in good form, and Moore was impressed by the Lancashire side.
"For me they're the best team we've played this season, although we were expecting that because they've got a system, they're a settled team with a rhythm to them and they've got players in offensive positions so it makes it even sweeter," he said. "Credit to the players because they took a lot of information on in the last two days.
"The gameplan was to get the ball wide, cross into the box and it was great to see Jack Hunt deliver it ona sixpence for Lee Gregory. I'm please for him because he worked absolutely tirelessly and you want to see your No 9 score goals."