Jason Bourne (Matt Damon) uses a SIG Pro SP2022 in Moscow when he is accosted by the Russian police in a pharmacy. He later has one in New York, seen "Mexican-carried" in his waist. This interchanges with a Glock when he is questioning Dr. Hirsch about his past. Neal Daniels (Colin Stinton), CIA station chief in Madrid, takes a SIG Pro when he goes on the run. One of the CIA agents sent in "heavy" to Daniels' office in Madrid has a SIG Pro with a camera attached. Bourne beats him up and takes it.
Glock 19
The CIA agents pursuing Bourne in London and Madrid carry Glock 19 pistols. An NYPD officer carries a Glock 19 as well.
Beretta 92FS
One of the CIA agents attempting to apprehend Simon Ross at Waterloo Station has a Beretta 92FS. Jason Bourne (Matt Damon) takes one from a Tangier police officer when chasing Desh in Morocco.
Look close and you'll see it's a Beretta Non-Gun. -- The Specialist.
The CIA agents in New York, including Noah Vosen (David Stratharn) and Pamela Landy (Joan Allen), carry Glock 17s. Jason Bourne (Matt Damon) also carries a Glock in New York City. Bourne's flashbacks to joining the Treadstone program show him with a Glock 17. Many NSA agents also use the Glock . One of the agents that hunt Bourne down in Sewell & Marbury also uses it.. Bourne then takes one of the Glocks and then uses it to threaten Nikki. It often changes into a Sig Pro while threatening Nikki too.
Paz (Edgar Ramirez) carries a Beretta 92SB when chasing Bourne through the New York training facility and eventually in the one-sided standoff in the end of the movie.