The males were arrested for affray, criminal damage, assault on police and causing a public nuisance.
Various road closures were put in place during the siege.
During the incident, a police inspector suffered head injuries which resulted in him being hospitalised.
Although serious, his injuries are not thought to be life-threatening.
The two males were also arrested on suspicion of robbery and actual bodily harm following an incident whereby alcohol was stolen from a nearby shop.
Two people were injured during the robbery and were treated at the scene.
Chief Inspector Glansfield from Humberside Police said:
“Incidents of this nature are highly disruptive to our communities.
“Our officers responded quickly to the initial reported robbery, and then to the scene of the rooftop siege, on a property of which the men had no connection to.
“Such events require large amounts of resources to ensure a safe resolution and to protect everybody affected in the locality.
“Often, as in this case, the damage left behind can be extremely distressing from those living in the area.
“One of our officers also sustained injuries as he was trying to go about his business protecting our communities. We will never tolerate these acts towards our people.
“I wish to thank the local residents for their patience during the disruption and encourage them to speak to the teams still in the area if they have any concerns or information they wish to share.”