Leverkusen needed a win to join fellow German clubs Bayern Munich and Werder Bremen in the last 16 and they broke through the resolute Dynamo defence when Juan was left unmarked to head in from a corner six minutes into the second half.
Bernd Schneider rounded the keeper with the one moment of true class to set up Ukrainian striker Voronin in the 77th minute and Babic tucked a shot under the keeper four minutes from time to complete the win.
Victory sent Leverkusen through as group winners ahead of Real Madrid thanks to a better head-to-head record while Kiev, third in the group, now go into the UEFA Cup.
Ajax also qualified for the UEFA Cup after finishing third in Group C with a 2-2 draw against Bayern Munich on Wednesday. The Dutch outfit pipped Maccabi Tel Aviv for a place in the last 32 of the UEFA Cup because of a better head-to-head record after both teams finished with four points from six games.
Roy Makaay gave Bayern a ninth minute lead but midfielder Tomas Galasek equalised seven minutes before the break. Striker Nicolae Mitea then put Ajax ahead in the 64th minute before Michael Ballack headed Bayern level 12 minutes from time.
In the other Group C game Maccabi Tel Aviv battled valiantly with Juventus for a 1-1 draw on Wednesday but the result was not good enough to keep their European season alive and they finished bottom of the group.
Maccabi took the lead with a Barukh Dego penalty in the 30th minute after Emile Mbamba was brought down by Fabio Cannavaro.
Juve equalised when Alessandro del Piero struck with a close-range shot in the 71st minute.
A rejuvenated Olympique Lyon, spearheaded by young Brazilian striker Nilmar, outclassed Sparta Prague 5-0 to finish top of Group D.
Determined to finish the pool phase on a high note, the three-times French champions took an early lead thanks to Ghana’s Michael Essien, who nodded in from a Florent Malouda cross in the seventh minute. Lyon’s constant domination was rewarded again in the 19th minute when Nilmar took advantage of a huge blunder by Sparta goalkeeper Jaromir Blazek to make it two from close range. The 20-year-old Brazilian striker sealed victory in the 51st minute and young substitutes Sylvain Idangar and Bryan Bergougnoux completed the rout with late goals.
Lyon, already certain to qualify, had fielded almost a reserve team.
Lyon finished top on 13 points as Manchester United could only manage second, on 11 points, after their 3-0 defeat at Fenerbahce.
The Liverpool-Olympiacos game may have monopolised the excitement last night but last season’s losing finalists, Monaco, took care of their own business in impressive fashion, powering their way into the knockout stages of the Champions League with a crushing 5-0 win over Deportivo La Coruna in Group A.
Didier Deschamps’ side soaked up some early pressure from Depor at the Riazor then produced a high-class display of finishing to hit the Galicians with three goals in the space of 18 minutes before the break.
Uruguayan Ernesto Chevanton completed a slick passing move to fire home the first, defender Gael Givet added another when he hooked in after a corner and Argentine striker Javier Saviola made it three with a coolly taken strike two minutes later.
Monaco completed their first win in Spain in emphatic fashion after the break when defender Douglas Maicon stabbed in from close range from a corner and substitute Emmanuel Adebayor guided home unopposed after a great pass from the outstanding Chevanton.
Deportivo, who were already condemned to finish last in the group, ended their campaign ignominiously, not having scored a single goal.