"We are not happy with the results and the coaching team is to be sacked and replaced by foreign staff," read a statement on the Iraq FA Facebook page (www.facebook.com/iraqfa).
"The FA will work with the Iraqi government and Iraqi Olympic Committee to provide funds for a replacement."
Shenaishil's departure follows that of United Arab Emirates coach Mahdi Ali, who quit after a 2-0 loss to Australia in Sydney in the same round of matches effectively ended his team's dreams of qualifying for Russia.
Thailand's Kiatisuk Senamuang also stepped down in the wake of the 4-0 thrashing by Japan that ended slim Thai hopes of reaching the finals for the first time.
Shenaishil led Iraq to the semi-finals of the 2015 Asian Cup in a previous stint in charge and, after a spell at Baghdad club Al-Shorta, returned to mastermind the bid to qualify for the World Cup finals for the first time since 1986.
Hampered by having to play their "home" matches in neutral venues for security reasons, the Iraqis were always going to struggle to clinch a ticket to Russia after losing their first three qualifiers of the third round.
The 1-0 loss to the Saudis on March 28 left the 2007 Asian champions fifth in Group B with four points from seven matches, nine points behind third-placed Australia and 12 in arrears to leaders Saudi Arabia and Japan.
The top two teams qualify directly for Russia, while third place offers a further berth via a playoff against the similarly placed team in Group A and an intercontinental tie against a team from the Central and North America Confederation.
(Reporting by Nick Mulvenney in Sydney, editing by Peter Rutherford)
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