Carlo Ancelotti's Bayern, who are no longer top in Germany, are next up at the Allianz Arena on Saturday and Leverkusen will travel to Munich in buoyed spirits.
Their 1-1 draw at CSKA Moscow on Tuesday, and Tottenham Hotspur's 2-1 defeat at Monaco, means the Germans, not Spurs, will reach the knock-out phase from Group E.
Kevin Volland, on the fringes of the Germany squad, scored Leverkusen's crucial first-half goal and hit the post late on in Moscow.
Like the rest of the Leverkusen squad, Voeller was following the Monaco-Spurs game on his smart phone when the team flew out of Moscow after their draw.
A cheer went up on the plane when the result was confirmed from Monaco.
The squad were dreaming of facing Real Madrid or Juventus in the last 16 after touching down at 1.42am (0042 GMT) following the three-hour flight.
"We are all very happy," said Voeller as the result was a welcome tonic following Friday's defeat to new German league leaders RB Leipzig.
"A result like that does you good, straight after the 3-2 defeat to Leipzig.
"For us, it was no foregone conclusion that we would reach the last 16 and it's unusual for us to progress from such an even group ahead of time.
"We're unbeaten in five Champions League games, which I see as a positive," added Leverkusen's director of sport following four draws and a single away win against Tottenham.
The 56-year-old admits he would have "signed with blood" if he had been offered a deal to qualify after Leverkusen drew their first three European games.
With a home game against group-winners Monaco still to come, this is the seventh time Leverkusen have qualified for the last 16.
The bonus of an extra six million euros ($6.3m) is also welcome for the club's coffers.
Leverkusen coach Roger Schmidt gave his players Wednesday off and on Thursday work starts for Saturday's match in Munich.
For the first time in 14 months, Bayern are no longer top of the Bundesliga table and lag three points behind new leaders RB Leipzig.
After last Saturday's 1-0 defeat at Borussia Dortmund, Bayern will be eager for a win over Leverkusen, but Schmidt also badly needs a good result at the Allianz Arena.
His side have won just four of their last 10 games and Volland's goal to take a precious point in Moscow eased some of the pressure on him.
"The last few weeks have not been so easy for me personally, there has been a lot written, and such a goal is good for self-confidence," said Schmidt.