The Football Association will investigate the incident and anybody found guilty of hurling bottles onto the pitch will be banned for life by the club.
A joint statement from Millwall chairman John Berylson and Fan Director Peter Garston read: "On Saturday, a wonderful game of football at The Den was overshadowed by the actions of a handful of mindless idiots who threw bottles onto the pitch.
"The newspaper match reports and TV coverage made little mention of the football, and once again the name Millwall was linked in people's minds with hooligan behaviour. This has to stop.
"As a club we have made tremendous progress over the past three years on and off the pitch. This cannot be allowed to be undermined by a minority who apparently believe they can do as they like.
"We had planned to open the lower tier of the North Stand for one of the big games we have coming up at The Den. In the light of what happened here at the weekend we will not be doing so, which hampers our attempts to increase our attendances and hits us financially.
"We pride ourselves in the passion of our support and the atmosphere created at our ground. But there are boundaries which cannot and must not be overstepped."