The shipment was flagged off from the Kandla port in Gujarat with External Affairs Minister Sushma Swaraj and her Afghan counterpart Salahuddin Rabbani joining the ceremony through video conferencing.
"The shipment of wheat is a landmark moment as it will pave the way for operationalisation of the Chabahar port as an alternate, reliable and robust connectivity for Afghanistan," the Ministry of External Affairs (MEA) said in a statement.
In June, India and Afghanistan had launched an air freight corridor between the two countries to boost trade as Pakistan has been refusing land transit access through its territory.
"I am extremely delighted that today we have joined on a momentous occasion for the people of our three countries and the region," Ms Swaraj said, terming the move as an important step in realising the shared aspiration to carve out "new routes" of peace and prosperity.
The consignment will be transported to Afghanistan from Chabahar through land route.
Ms Swaraj also reiterated India's continued commitment to support reconstruction, capacity building and socio-economic development of Afghanistan, including under the framework of the New Development Partnership announced last month.
"The wheat that is leaving the Indian shores today, is a gift from the people of India to our Afghan brethren. It is testament to the continued commitment of the government and the people of India to support our Afghan brethren in building a normal, peaceful, prosperous, secure and bright future for themselves," Ms Swaraj said.
The External Affairs Minister also renewed commitment to work closely with regional and international partners to bring peace, security, stability and prosperity in Afghanistan.
The Chabahar port is expected to open up new opportunities for trade and transit from and to Afghanistan and enhance trade and commerce between the three countries and the wider region.
"The people of India, Afghanistan and Iran have been connected through centuries; shared commonalities of art and culture, ideas and knowledge; language and traditions. Today, we are rejuvenating these connects and commonalities. I believe that this is the starting point of our journey to realise the full spectrum of connectivity," Ms Swaraj said.
Ms Swaraj and Mr Rabbani welcomed the fact that this is the first shipment that would be going to Afghanistan through the Chabahar port after trilateral agreement on Establishment of International Transport and Transit Corridor was signed during the visit of Prime Minister Narendra Modi to Iran in May 2016, the MEA said.
It said six more wheat shipments will be sent to Afghanistan over the next few months.
India and Iran have already expressed commitment for early completion of the work on the Chabahar port project.
The Chabahar port, located in the Sistan-Balochistan province on the energy-rich Persian Gulf nations southern coast, lies outside the Persian Gulf and can be easily accessed from India's western coast, bypassing Pakistan.
The port is likely to ramp up trade between India, Afghanistan and Iran in the wake of Pakistan denying transit access to New Delhi for trade with the two countries.
India has been closely working with Afghanistan to create alternate and reliable access routes, bypassing Pakistan.