Leverkusen would have gone a point clear at the top with a win but hosts Frankfurt put in a strong first half performance to quickly take control.
They struck twice through Paciencia before Leverkusen managed to even find their footing in the game.
Paciencia fired Frankfurt into the lead in the fourth minute and doubled it 13 minutes later with a penalty, sending keeper Lukas Hradecky the wrong way.
Frankfurt keeper Frederik Ronnow then made a string of superb saves in the second half, including stopping a point-blank header form Lucas Alario, to protect their two-goal cushion before Bas Dost added a third in the 80th.
Victory lifted Frankfurt into seventh spot on 14 points, ahead of Leverkusen on goal difference.
Leaders Borussia Moenchengladbach, on 16 points, travel to Borussia Dortmund on Saturday. Champions Bayern Munich, in third place also on 14, face Augsburg in the Bavarian derby. (Reporting by Karolos Grohmann, editing by Pritha Sarkar)