Police Federation for Northern Ireland chairman Mark Lindsay said: "Thankfully, no one was injured, but of course there was wholesale disruption because of the actions of mindless terrorists and their misguided supporters.
"Lives were needlessly disrupted and put at risk. A local community was left traumatised and in the end nothing was achieved by this act of madness.
"Officers were once again targeted by dissident republicans, but that won't deter them from doing their job in a professional manner.
"People who want to help their communities should isolate the perpetrators and come forward with any information which would assist in their arrest."
The pipe bomb was thrown at a police vehicle passing nearby Charlotte Street, where a number of residents were forced to leave their homes until the early hours of the morning.
PSNI district commander Mark McEwan said: "We are investigating all offences committed at the bonfire in the Bogside last night, including a serious incident where a viable pipe bomb-type device was thrown at a police patrol."
Hundreds of spectators gathered on the Lecky Road on Monday night at the massive pyre.
The stench of burning rubber from dozens of smouldering tyres hung in the air yesterday as glass crunched underfoot and a clean-up operation began.
Angry residents opposed to the bonfire were furious that a small number of mostly youths had effectively closed down the entire area.
One man said: "Look at the shape of this place now. You have tourists piling in here over the past two days taking pictures. They will go home and tell their friends there are a bunch of madmen in Derry who light bonfires in the middle of the road.
"I don't know how many different ways these cubs need to be told the bonfire isn't wanted.
"You could shout it from the rooftops and they wouldn't take a blind bit of notice because it's their way or no way.
"Something needs to be done. I am not saying it is going to be easy, but this cannot be allowed to happen again next year - it is a disgrace."
DUP MLA Gary Middleton and two of his party colleagues came under fire from a petrol bomb as they watched the bonfire from the Derry Walls.
He said: "What I witnessed was a very dangerous situation, which was not being managed in any way.
"I accept that if the police had gone into the Bogside after the bonfire was lit it had the potential to make things worse, but I don't think it should have been allowed to get to that stage in the first place.
"The impression I got was that this was a small number of people holding the rest of the community to ransom. This must not be repeated. I think now is the time to begin that task, and the young people need to be brought into the process.
"It is the only way to prevent this next year again."
Sinn Fein's Raymond McCartney suggested the young people involved in the bonfire were manipulated. He said: "There was an opportunity to avoid these problems through dialogue.
"Unfortunately, that failed because people absented themselves from that process or effectively scuppered it by acting as cheerleaders for anti-community behaviour.
"This situation was dictated by a tiny group of young people who are being exploited by more sinister elements clearly determined to act against the wishes of the local community."