The proposal was approved by 170 votes in favor, 31 votes against and 7 abstentions.
The ratification obliges the Energy Ministry and the Ministry of Industry, Mine and Trade to implement the water transfer project and tasks the vice presidency for scientific affairs to oversee their work.
The project involves desalination of the sea water for drinking and other uses in Sistan and Balouchestan, where most areas have a dry hot weather with little annual rain.
Opponents are worried about the environmental impact of the project.
The proposal, which also needs a go-ahead from the cabinet, was first tabled in March 2016.