During the identification parade before judicial magistrate on Saturday, the witness identified Aziz as primary suspect.
Identity of the eye-witness has been withheld for security reasons. Aziz is currently under physical remand of security forces in relation to his suspected involvement in over 20 terrorism cases.
Ms Lobo was shot and wounded in Karachi on April 16, with leaflets found at the scene claiming the attack on behalf of the Islamic State group.
Lobo was on her way to the college when her car came under attack by two armed assailants riding on a motorbike on Shaheed-e-Millat Road.