A team spokeswoman confirmed on Monday that the highly-rated former Renault chief designer, who arrived at the team only last month, had left and said it was a personal decision.
Jordan are hurrying to complete their car before the start of the season in Australia on March 6 but the takeover by Russian-born Canadian businessman Alex Shnaider has led to obvious overlap.
His Midland Group were planning to enter their own team in the championship from 2006 and had already commissioned Italian chassis-builder Dallara to design a car.
Smith is a close associate of Toyota technical director Mike Gascoyne, working for him previously at Jordan and then Renault, and there was speculation when he returned to Jordan that it would merely be a staging post before a move on to Toyota.
