The parents, both armed with handguns, then pursued him to a nearby petrol station where a struggle ensued.
Police said that both parents are licensed handgun carriers.
While the man went inside to ask staff to call police, his wife held the man at gunpoint outside.
The father told police that he was forced to shoot the man when he grabbed his wife's gun and pointed it at her.
He told ABC13 that he shot the alleged peeping Tom four times, including two shots in the chest and one in the stomach.
He survived the shooting and was transported to hospital in a critical but stable condition.
Tragically, the desperate dad said that his daughter had previously complained that someone was watching her through her window - but they had not believed her claims.
The case has now been turned over to the Harris County District Attorney's Office, which will decide whether to file any charges.