This question came up on the Science Fiction and Fantasy Stack Exchange, and there's a canonical answer now in Agents of S.H.I.E.L.D. material. Here is my answer from there, quoted word for word.
This was apparently explained in the pilot episode of Agents of S.H.I.E.L.D. where they depict a Chitauri neural link that Agent Grant Ward liberates from Vanchat in Paris.
This S.H.I.E.L.D. evidence sheet provides more details (which, despite the numerous misspellings, seems to be an official artifact of the series).
The Chitauri Neural Link is a communication pathway between the Chitauri soldiers and their technology. Neural links are often used to assist, augment, or repair cognitive or sensory-motor functions. They can also be used as a type of mind control and manipulation prostheses. The link connects all Chitauri to each other, to their weapons, and to their vehicles. All information and commands are routed through the Mother Ship which guides the Chitauri forces during their invasion. This makes them a rather formidable fighting force.
The Chitauri Mother Ship acts as the main communication hub for the invading Chitauri forces. Not only does it allow their soldiers to communicate but also directs them in battle. The Chitauri are of a hive mind, a singular collective of alien cybor-like creatures working as one to overwelm their enemies.
Fury orders Iron Man to intercept a nuclear bomb and dispose of it. Stark takes it to the portal and blows up the Chitauri Mother Ship, severing the link between the Mother Ship and it's army, thus killing all the Chitauri in New York with a immense feedback discharge.