Carles Perez scored the only goal of the game, as the Giallorossi got back to winning ways and earned themselves a slender advantage heading into the second leg of the last-32 tie.
The two sides meet again in a week at the Ghelamco Arena.
"The most important thing was to win and keep a clean sheet," Fonseca said.
"It's not easy at the moment, but the players have battled and worked hard to improve. We haven't yet rediscovered the level of confidence that we previously had, but the players want to change that."
Did Bryan Cristante move between midfield and defence because of the opponents' attributes or to make the team more solid?
"As a team, they tend to press with two forwards and we saw how they find it more difficult against a back three. We considered that as a solution to prevent them from pressing high in that part of the pitch. I think we did well in terms of building the play, but there weren't enough passing lines. We kept it simple up front when we actually should have taken more risks, particularly when we got through the first line of the Gent press."
Right now are you mostly pleased about the result or the fact that you've kept a clean sheet?
"It was important for the team's confidence levels not to concede a goal, but I can't say we produced a great performance. It was very important to win today, however, and the same thing goes for keeping a clean sheet. We will look to get a good result in the second leg and also produce a quality display."
What did you not like?
"When there's no confidence to play our game, we mustn't take too many risks because the passing lines aren't the same as they were a month ago. The players tried to do these things well and it was very important to win today. We're still lacking that confidence to close games out at the right time and get our passing lines right. I want to mention our fans, who were fantastic tonight. They understood that the team needed support and they did just that. I wanted to praise them for that."
At times like this, is it better to make adjustments or continue down your own path?
"I'm not against change. I've made more changes this season than in the rest of my career. Having said that, we don't need to change much at the moment. We need to improve what the team knows how to do. I've thought about changing the formation during games, but didn't want to send out signals that might not help the team. The players have always been confident defensively, which is why I haven't changed it. I'll have no issue doing it when it's necessary."
Maybe you'll get back on track when the passing is better and more daring?
"Yes, that's true. I always think the best way to defend is to keep the ball, but to play like that, you need players who are confident and want the ball. It's not the right time to play that sort of game for us. You don't need to keep the ball just for the sake of it, but you need to try to do something with it. The players decided not to take big risks tonight, even when there were chances to push on and change the game. Pau Lopez was on the ball so much, but we had to play it long because our passing lines weren't in place and we resorted to long balls."
Were you surprised that Lorenzo Pellegrini was whistled?
"No. I think that Pellegrini is a very important part of this team. If he's not in great form, we have to support him because he's a youngster who feels the responsibility more than others. I've spoken to him about this. If there's a member of the team who loves Roma like nobody else, it's him. He's really felt the responsibility during this period. We have to help him. He has to rediscover his confidence and we have to understand that he's young, how much he loves Roma and carries the feeling of responsibility. He's done so much for Roma this season and we can't forget how important he is to the team."
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