Moore gave credit to the hosts for their performance and said his side did not look like their usual selves in his interview after the game.
The Owls' boss also spoke about Wednesday's attacking and defensive performance, their fixture pileup and gave a fitness update on his squad including George Byers and Lee Gregory.
On Wednesday's attacking performance
"We weren't ourselves today, we weren’t clean enough with the ball at our feet and the game just ran away from us.
"We got into some wonderful threatening areas and then mis-controlled it or played a slack pass, we were hesitant to take the shot on."
The Imps defended expertly well throughout the game, limiting Wednesday to chances from outside the box for most of the game.
However, The Owls were also partly responsible for the lack of openings they had to score in the game, as Callum Paterson was isolated until he was taken off in the 70th minute.
The visitors provided no real immediate attacking threat on the day for most of the game, which was reflected in the score line.
Moore was keen to stress that this was in stark contrast to Wednesday's recent attacking performances, which had seen them win seven of their last eight games.
On The Owls' defensive showing
"We left areas where we were allowing ourselves to be exposed.
“If the ball is bouncing twice from a set play then you’ve got to be asking questions, whether or not that’s tired minds I don’t know.”
Moore was referring to the opening goal for The Imps, in which the ball was flicked onto the back post for a corner for Marquis to tap in, all without a real challenge from a Wednesday player.
It was a disappointing display from the hosts overall defensively, conceding three goals to a struggling Lincoln side.
Sam Hutchinson played reasonably well heading the ball off the line to deny Tom Hopper in the second half and making a few good challenges to keep The Imps at bay.
Overall however, it was a shaky defensive display, which often saw the hosts have far too much time on the ball on the edge of the box.
It was a defensive display that Moore and his players will want to forget, having now conceded five goals in their last two games.
On Lincoln and League One
“Credit to Lincoln, they worked extremely hard today and fully deserved the win, they didn't allow us to build any momentum in the game.
"At this stage of the season you see results like this because the finishing line is in sight and people know what's expected."
The Imps produced a fantastic performance to secure what could be a huge three points in the context of their season.
A brace from Marquis and a driven shot by Norton-Cuffy were enough to secure a superb victory for Micheal Appleton's side.
They will now be hoping to produce performances of similar quality, which will be a huge boost in their fight for survival.
Moore denied that the result had been as a consequence of any complacency from his side, saying that any team had the ability to win in League One.
On his side’s fixture pileup
“Today we were just a bit off it, whether that’s because it was a three-game week or because we didn’t really change it around today, maybe it was just a game too far for us.
"Looking at the balance of play and the fatigue in our side, as a manager you just know when your side's not full tilt and today we wasn't."
The third game in the space of a week caught up with Wednesday, as the players look tired and off the pace following their victories against Charlton Athletic and Burton Albion on Saturday and Tuesday respectively.
The noticeable difference from the 5-2 win against Burton on Tuesday night was that when The Owls threw away their two-goal lead at Hillsborough, they kept going and managed to ensure an emphatic victory by full time.
Whilst there was an improvement from Wednesday after going a goal down on Saturday, it was not sustained, and they struggled to compete in the second half.
They did not seem to have the fitness to challenge a buoyant Lincoln side during the latter stages of the game in particular.
On the fitness of his players
“I look at the run that we’ve been on and it’s been the same group of players that have been turned around to play in those games.
“Even though we had Fisayo [Fisayo Dele-Bashiru] and Greggers [Lee Gregory] come back today, I don’t think I’ve got [a selection dilemma] at the moment.”
Moore suggested that the lack of depth in the squad currently due to the injury crisis at the club caught up with them, as the depleted Wednesday side was devoid of answers at the LNER Stadium.
Even the introduction of club top scorer Gregory just past the hour mark was not able to help the South Yorkshire based club get back into the game.
The striker returned to the squad today after a spell on the side-lines with a foot injury.
Dele-Bashiru was also able to make his return having been out injured since early February.
Moore said that the pair would have a week to prepare to play a full 90 minutes next week.
He was not sure whether they would be able to start next week, but said they would use the week to try and be fit enough to start game.
Despite this, there are still several first team players who remain injured and unavailable to Moore, leading to him admitting that he does not yet have the players to have the selection dilemma that he may well have when they all return to fitness.
Moore suggested it would be around two weeks before the bulk of his absentees return from injury.