After a less-than-convincing performance in Bosnia eight days ago, the Eagles won 2-0 at Selhurst Park in the second leg to keep up their aims of winning European silverware for the first time in their history.
With the top eight sides from the League Phase now re-entering the competition, their task is a little tougher.
Top seeds Strasbourg, unbeaten in the League Phase, and under new management in the form of Gary O'Neil, will take on Rijeka after the Croatian side beat Omonia in both legs to progress.
Perennial semi-finalists Fiorentina, who survived an almighty scare to squeak past Jagiellonia on Thursday, have been given another Polish test in the form of Rakow.
Sparta Prague, who will be confident of progressing after they were pitted against AZ Alkmaar, whilst third seeds AEK Athens will take on Celje.
Elsewhere, Rayo Vallecano - the only Spanish side in the Conference League this season - will face Samsunspor, whilst Shakhtar, sixth in the League Phase, takes on Lech Poznan.
The final will be played in Leipzig on Wednesday, May 27th.
Conference League last 16 draw in full:
The first leg of these ties will take place on March 12th, and the second legs will be played a week later. The first team in the pairs will play the first leg at home.
Lech Poznan v Shakhtar
AZ Alkmaar v Sparta Prague
Crystal Palace vs AEK Larnaca
Fiorentina v Rakow
Samsunspor v Rayo Vallecano
Celje v AEK Athens
Sigma Olomouc vs Mainz
Rijeka v Strasbourg
Road to Leipzig paved out
With the draw now set all the way to the final in Leipzig in May, the Conference League teams can glimpse at their future opponents.
For Fiorentina, who are still striving for success in the competition, they could face Crystal Palace in the quarter-finals, before a potential semi-final against Sparta Prague.
For the lowest seed, Sigma Olomouc, if they can upset Mainz, a trip to Strasbourg will be on the cards. For the French outfit, who have designs on winning this competition, their likeliest semi-final opponent is Rayo Vallecano of LaLiga.