It was confirmed last week that the 42-year-old intended to resign if the club did not earn a "positive result" against Braintree.
The Minstermen ended up being restricted to a 1-1 draw at Cressing Road, and as a result, McNamara has relinquished his role as permanent boss.
A statement from York read: "After purposeful discussions it was agreed that results and performances, in the main, have not been acceptable nor have they achieved the high standards expected.
"In order to assist the managerial transition period and to accommodate a thorough identification, interview and appointment process, the chairman has asked Jackie McNamara to train and prepare the team until a suitable candidate has been determined. This process should be completed within two weeks."
The Scotsman took charge of York in November last year.