But the Gunners, who hit the woodwork twice, conceded a last-gasp equaliser from defender Tomas Holes after a corner, giving Slavia a vital away goal and the advantage heading into the return fixture.
And that means the north London outfit – who sit 10th in the Premier League – have left themselves a huge task next week as they look to reach the final four at the expense of a team who have already eliminated Leicester and Rangers.
A clearly disappointed Arteta, who appeared to keep his Arsenal players in the dressing room longer than usual after the full-time whistle, told BT Sport: “The game was under control, we had the goal we wanted. We missed some big, big chances.
“Then we played two or three balls in areas we shouldn’t, we put ourselves on the back foot. We concede the corner and from there, they put a lot of bodies in there and anything can happen.
“In this competition we know the subs have a lot to say. They made the impact we needed but unfortunately we didn’t capitalise with the result that we wanted.
“It was difficult because they are a really good opponent, have beaten some big teams and are really difficult to play against.
“The way they do it is a lot of duels, a lot of man to man situations and you have to be able to resolve them. What happened is when we could do that we could create a lot of chances.
“I think we were very effective in our high press. We regained a lot of balls there. It’s true they have a lot of capacity in the duels, if they win it to run into the transition but I think we controlled that pretty well.
“It’s more about the final result. That leaves a difficult taste. We need to win the game [in the second leg]. The mindset is to go there to win the game. We need to score and we know that. We’ve done it in the past and we know we need to do it again.”
Arsenal legend Martin Keown was equally as disappointed with the result, and was underwhelmed by the performance of summer signing Thomas Partey in central midfield.
“They had good opportunities in the game, Lacazette with a great opportunity, then they just got ahead through Pepe after making the changes. The substitutes gave Arsenal much more energy.
“Then the marking for the corner is atrocious or non-existent. Gabriel, in the build-up to that there’s a bit of panic, a nervousness.
“As you say, no clean sheet in 14 games for Arsenal and it showed tonight. When they needed it most, to keep a clean sheet in the last five or 10 minutes, they just couldn’t do it.
“Partey, as well, tonight, was another player that really disappointed me. Watching it live here, and we’re not getting into the stadiums that often, he didn’t look like he had the legs to get around the pitch.
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“But that’s an area of the pitch that I would’ve thought by now, he would be bossing.
“It’s going to be difficult now for Arteta. He’s made a lot of changes at the football club, a lot of people have been allowed to go, and this is his team now, essentially.
“There have been a lot of problems at Arsenal over a number of years, certain players coming in and out at the football club, so it’s not all at his doorstep.
“But he’s in charge now, and he’s not quite getting the reaction out of the team. He was disappointed at the end there. He’s encouraging people to play, then at the end when he doesn’t want them to play, it’s a mixed message, isn’t it?
“They’ve got to do the right things at the right times and they’re making sloppy mistakes and it cost them tonight.”
Arsenal return to action against bottom-of-the-league Sheffield United on Sunday (7pm) before their trip to the Czech Republic next Thursday for their second leg against Slavia.