The Portuguese forward fired Frankfurt ahead inside five minutes as he latched on to a Danny Da Costa pass and held off two defenders to stroke the ball under Lukas Hradecky.
Paciencia won a penalty on the quarter-hour when his shot was blocked by the hands of a sliding Aleksandar Dragovic, rolling home the spot-kick to double the lead for the hosts.
Eintracht goalkeeper Frederik Ronnow, deputising for the injured Kevin Trapp, kept Leverkusen at bay with a string of stops from Karim Bellarabi, Lucas Alario and Kai Havertz.
Leverkusen were awarded a penalty midway through the second half for an apparent handball by Djibril Sow but the decision was correctly overturned following a VAR review.
Dutch striker Bas Dost wrapped up the victory for Frankfurt 10 minutes from time as he brushed off Dragovic to net his third league goal of the season.
Eintracht moved level with Leverkusen as part of a cluster of six teams on 14 points, two adrift of leaders Borussia Moenchengladbach.
Marco Rose's Gladbach go to Borussia Dortmund while second-placed Wolfsburg travel to RB Leipzig.
Defending champions Bayern Munich will attempt to bounce back from a 2-1 loss at home to Hoffenheim when they visit Bavarian neighbours Augsburg.
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