Vakhtang Tchanturishvili scored in the 73rd minute for the home side to give them a 1-0 win in the second-leg and see the game into extra time.
However, it was the Czech side who came out on top in penalties as they progressed to the league phase, with Rangers eliminated from Europe.
Derek McInnes named an unchanged starting line-up from last week’s 1-0 victory in the first-leg.
That meant Pandur started in goal behind a back four of Dujon Sterling, Emmanuel Fernandez, Olwethu Makhanya and James Penrice. Dan Neil captained the team in midfield alongside Vanja Dragojevic and Tochi Chukwuani.
Ryan Naderi, who scored the only goal in the first-leg, led the line once again with support in the wide areas from Daisuke Yokota and Djeidi Gassama.
The hosts were also unchanged from their visit to Ibrox as the teams faced-off for a place in the league phase.
It was Jablonec who had the first real sight of goal in this one as Jan Suchan sent the ball into the path of Lamin Jawo but the striker put his right-footed shot just wide of the target in an early warning for Gers.
At the other end, Tochi Chukwuani had a header saved by the goalkeeper after he got on the end of a delivery from James Penrice.
There was another chance for Jawo as the game approached the half-hour mark. This time he glanced a cross from Suchan but it was a comfortable save for Pandur.
McInnes made a triple change at the break as he introduced Connor Barron, Findlay Curtis and Lawrence Shankland in place of Dan Neil, Daisuke Yokota and Djeidi Gassama.
A short corner for the home side saw them threaten early in the second-half, with Suchan’s shot gathered by Pandur.
Aasgaard was next to be introduced as he replaced Vanja Dragojevic for the final half an hour in the Czech Republic.
Jablonec were pushing for a goal in the opening period of the second-half with the home supporters getting a lift inside the stadium.
The pressure paid off for the home side as they took the lead in the 72nd minute through Vakhtang Tchanturishvili. It was an individual effort from the forward, who cut inside from the right, and sent a powerful strike into the bottom corner.
Sebastián Nebyla had a chance as a quick free-kick saw him race towards goal, but he couldn’t keep his effort on target.
Rangers were unable to carve out another opportunity as the referee blew time on the 90 minutes and the match went into extra time.
Findlay Curtis sent a header wide early in added time after a positive move by Gers, with the cross coming in from Nedeljkovic on the right, before Antonín Růsek flashed a shot wide from distance for the Czech side.
Jablonec came close in the 103rd minute, with Jan Chramosta sending a ball across the face of goal, with Antonín Růsek coming in at the back post but thankfully for Rangers it was just in front of the striker and bounced beyond Pandur’s left-hand post.
There was a final change for Rangers in half-time of extra time as Dujon Sterling was replaced by Bojan Miovski.
Again Jablonec threatened, as Jan Chramosta’s shot was inches wide of the post.
Rangers had a chance of their own in the final minutes of extra time as Shankland headed a Thelo Aasgaard cross towards goal, but it was deflected over the bar to send the game to penalties.
It was captain Shankland who stepped up to the first spot-kick and it was a fantastic set-piece as he powered it beyond Jan Hanuš. Růsek levelled for the home side, before Miovski confidently slotted home his penalty too.
It was another strong penalty from Richard Sedláček to level it at 2-2 with Thelo Aasgaard the third player to step up for Rangers and it was another good set-piece.
Filip Zorvan saw his penalty saved well by Pandur, before Findlay Curtis sent his over the bar.
Nelson Okeke scored, before Penrice had his saved to set up a winning penalty for the home side, which Jan Chramosta finished to see the Czech side into the league phase.
RANGERS: Pandur, Sterling (Miovski, 105), Fernandez, Makhanya, Penrice, Neil (Barron, 46), Dragojevic (Aasgaard, 60), Chukwuani, Yokota (Curtis, 46), Gassama (Shankland, 46), Naderi (Nedeljkovic, 79).
Subs: Kelly, McGuire, McCrorie, Godfrey, Cameron, McCausland.
Jablonec: Hanuš, Tekijaški (Okeke, 85,) Tchanturishvili, Suchan (Zorvan, 79), Sedláček, Pavlovic, Cedidla, Sláma (Sobol, 79), Polidar (Chramosta, 64), Nebyla (Vecheta, 109), Jawo (Růsek, 64)
Subs: Mihelak, Okeke, Souček, Ahl, Novák