T David Haokip (23) and Lalminsang Khongsai (20) were apprehended after they surrendered before the probe agency, Deputy Commissioner of Police of South District said.
A man had on August 15 filed a complaint, saying the accused, along with others, "brutally attacked" a stray dog with bricks in Munirka village, packed the animal in a bag and fled the spot.
An FIR was registered under the relevant provisions of the Indian Penal Code and the Prevention of Cruelty to Animal Act, police said.
Another accused, James, is absconding police said.