UEFA fined Bayern 40,000 euros after travelling fans set off fireworks during their 2-1 win at Copenhagen in October. Bayern were given a suspended one-match ban from purchasing away tickets in December. The incident at Lazio triggered the ban.
The club will not appeal UEFA's decision, Bayern said in a statement.
"We have to accept this punishment. Not only were pyrotechnics set off, but also fired deliberately onto the field, directly endangering bystanders," Bayern CEO Jan-Christian Dreesen said.
"This was such an explicit violation of the conditions of probation that an appeal is unfortunately futile.
"The fact we now have to play away without the support of our fans is a big blow. A small group of individual offenders have done a disservice to all our supporters and the team."
Bayern beat Lazio 3-1 in aggregate to reach the last eight. The draw for the quarter-finals will take place on Friday.
The first legs will be played on April 9th and 10th, and the second legs are scheduled for April 16th and 17th.
