The Spanish winger, a January signing from Barcelona, clinched a first leg victory for the Giallorossi in the last-32 tie - marking his full debut with a fine first-half finish for Paulo Fonseca's side.
Roma had plenty of other chances to extend their advantage over the course of the game, but Thomas Kaminski in the Gent goal proved equal to everything thrown at him - with two particularly notable saves to deny Chris Smalling and Aleksandar Kolarov.
The two sides meet again in seven days, as the Ghelamco Arena hosts the second leg.
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It was a dream full debut for Perez, who needed less than 15 minutes to get off the mark in front of his new fans.
Edin Dzeko spotted the winger's run and played him in, with Perez making no mistake as he opened up his body in passed the ball home.
As the game continued both sides created chances, with Pau Lopez also occasionally called into action - with Vadis Odjidja testing him twice in quick succession. But it was the hosts who had the better sights of goal, only for Kaminski to make his presence known.
The Giallorossi are back in action on Sunday, as they host Lecce at the Olimpico.
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