Canizales was seemingly on his way to a points win against the Chinese challenger, who was fighting in only his second pro bout on the night.
With just seconds to go until the final bell, Canizales connected with two straight right hands to drop and stop Bin to wild scenes of celebration in Kuala Lumpur.
The ending time recorded at ringside was 2:59 of the twelfth.
At featherweight, Jhack Tepora won the interim WBA featherweight title with a ninth round victory over Edivaldo Ortega.
Tepora dropped Ortega and piled on the pressure, forcing the official to step in and save Ortega from further punishment.
Improving to 22-0, Tepora moves closer to a shot at Leo Santa Cruz, whilst Ortega loses for the second time in his career.
Claiming the vacant IBF flyweight title for his efforts, Moruti Mthalane defeated Muhammad Waseem via a unanimous decision after dominating the early going.
Waseem was too late to the party as the Pakistan star dropped and pressured Mthalane in the final two rounds but by then the damage had been done by the South African.
Using intelligent and measured boxing, Mthalane racked up the early sessions to regain the red strap he previously held between 2009 and 2012 with scores of 116-110 and 114-113 twice on the cards.
Earlier, Juan Elorde kicked off proceedings with a third round knockout of Ratchanon Sawangsoda in the super-bantamweight division, whilst at welterweight, Theena Thayalan and Siddharth Varma fought out a four-round draw.