Portuguese Paciencia, who scored for the second straight week in the domestic league and has netted another three goals in the Europa League qualifiers, found space down the right to fire home for the victory late in the game.
Earlier he had crossed for Dost, who signed on Monday, to cancel out Fortuna's first-half lead 13 minutes after the Dutchman came on as a substitute in the second period.
Eintracht now have six points from three matches.
Werder Bremen had to score three times against Augsburg to secure their first win of the season after the visitors twice came back from a goal down.
Yuya Osako's second goal in the 67th made it 3-2 and sealed the first three points of the season for Werder.
RB Leipzig are top on nine points from three games following their 3-1 victory at Borussia Moenchengladbach on Friday.
Bayern Munich crushed Mainz 05 6-1 on Saturday to climb to second on seven points while Borussia Dortmund are a point behind after a shock 3-1 loss at Union Berlin.