Kwara forced a 0-0 second leg draw away to AS Douanes of Niger in Niamey to advance 3-0 on aggregate after building a healthy lead at home last weekend.
But African debutants Remo, having exceeded expectations by holding 2005 Confederation Cup winners FAR Rabat in Morocco, fell 1-0 at home to bow out 2-1 on aggregate.
The crucial goal came 11 minutes into the second half when Ivorian Joseph Gnadou sprinted down the left, cut inside and unleashed a shot into the far corner of the net.
No Nigerian club has won the African equivalent of the UEFA Europa League with now defunct Dolphins coming closest by reaching the two-leg 2005 final, which they lost 3-1 to FAR.
Kwara are likely to face much tougher opposition in the round of 32 during October as they have been paired with two-time Confederation Cup title-holders Renaissance Berkane.
Berkane, who hail from the citrus growing northeastern region of Morocco, enhanced a growing reputation this month by surprising compatriots Wydad Casablanca to lift the CAF Super Cup.
The Orange Boys have reached three of the last four Confederation Cup finals, losing to Zamalek, then beating another Egyptian club, Pyramids, and South African side Orlando Pirates.
Elgeco Plus of Madagascar beat PWD Bamenda of Cameroon 1-0 in Antananarivo to pull of a surprise 2-1 aggregate victory.
Fenohasina Razafimaro scored the deciding goal on 60 minutes and the reward is a winnable showdown with Marumo Gallants, who are struggling in the South African Premiership.
The other South African challengers, African rookies Royal AM, left it late to seal a place in the next round at the expense of Mbabane Highlanders from neighbouring Eswatini.
Ruzaigh Gamildien scored on 89 minutes to clinch a 2-0 victory in the second leg and on aggregate after Mozambican Elias Pelembe had broken the deadlock just before half-time.
Next up for Royal, who are bankrolled by TV personality and businesswoman Shauwn 'Ma' Mkhize, are vastly experienced Zambian side Zesco United.