A police spokeswoman said the Armed Offenders Squad and other officers worked for several hours attempting to negotiate with the man, 49, to come down.
"A number of vehicles were damaged by items thrown from the roof.
"A police dog was injured during the incident, but his injuries are not believed to be serious at this stage.''
Police said no shots were fired during the stand-off, but distraction devices and a Taser was set off and the man was taken into custody about 1.10am.
"The man was taken to hospital as a precaution but was soon discharged and remains in police custody.''
He is now due to appear in the Hamilton District Court today facing charges including assault, robbery, wilful damage and injuring a police dog.
Police thanked members of the public and local community for their patience as officers worked to deal with last night's situation.