Caio Junqueira uses 2 handguns in the movie: a Glock, and a Taurus PT-92. The Glock could be a Glock 19, 23 or 25. It's most likely a Glock 25 in .380 ACP.
Taurus PT-92
This handgun is used both by the police and by the Drug dealers
Revolvers
Taurus revolver
André Ramiro uses both a Taurus PT-92, and a revolver, that I think is a Taurus model 83, although it is never seen close enough.
Submachine Guns
IMI Micro-Uzi
An IMI Micro-Uzi (or a Uzi pistol) is used by one of the drug dealers in a shootout.
Heckler & Koch HK94A3
A chopped and converted Heckler & Koch HK94A3 is used by Captain Nascimento in several scenes, as noted by its lack of paddle magazine release and barrel lugs, and the metal lower receiver.
INA Model 953
The INA Model 953, the Brazilian version of the Danish Madsen M50 SMG. Recognized by its stamped metal body which, literally, is held together by the barrel nut (which was known to come loose on its own, spilling the internal mechanisms on the ground). Brazil manufactured it in .45 ACP instead of the standard 9mm.
Captain Roberto Nascimento (Wagner Moura) carries several guns through the movie. One of them is an Colt SP1 with M16A2 hand guards, the rifle carried by most of the men of the BOPE in the movie.
FN FAL
An IMBEL Fz M/964 (FN 50-00 Brazilian license-build fixed-stock version) is used by the drug dealers as well as a DMR by at least one of the BOPE officers and a standard configuration by another.
Ruger Mini-14
Ruger Mini-14 rifles are used in several scenes by the drug dealers:
Unidentified rifles
In the opening scenes, Caio Junqueira opens fire with an unidentified scoped rifle. It might be an Imbel AGLC, but I can’t identify it with certainty. It's maybe IMBEL M/968 (old Czech or Belgian Mauser enhanced with new 0.308 barrel in the 60's).
IMBEL M968
The new BOPE recruits can be seen training with the M968 and other brazilian-made variants of the Mauser M908.
Shotguns
Companhia Brasileira de Cartuchos Model 586P
CBC Model 586P shotguns are seen in the hands of the BOPE agents.
Mossberg 500
A Mossberg 500 with wood furniture and a ventilated ribbed barrel as well as a standard model can be seen in the hands of BOPE officers.