Lithuania coach quits after Czech thrashing
Former Lithuania captain Zutautas, 39, had been in charge since February 2010 after replacing Portugal's Jose Couceiro.
"We have failed to win as many points as we wished. Since I, as a coach, failed to reach my goals, I'm finishing my work here," Zutautas said in statement.
Lithuania finished fourth out of five teams in Group I with just five points from eight matches. Their campaign began in promising fashion with a draw against Scotland and a shock victory over the Czechs in Olomouc.
But they picked up just one further point from a draw at home to perennial strugglers Liechtenstein.