A small Bronx evangelical church on Monday lost the final round of its 16-year legal battle to force New York City to permit religious worship services in public schools, setting the stage for the city to eject dozens of churches and religious organizations that have been using schools for prayer.

The Supreme Court announced that it would not review a lower-court decision that backed the city’s decision to ban the evangelical congregation, the Bronx Household of Faith, from holding its Sunday services at Public School 15, where it has worshiped since 2002.

As a result, the city said it would move to end the hundreds of prayer services that had been held in schools in recent years — some 160 congregations used school buildings for worship services in the 2010-11 school year alone — by Feb. 12, 2012.

“We view this as a victory for the city’s schoolchildren and their families,” Jane Gordon, the senior counsel of the New York City Law Department, said in a statement. She added that the Education Department “was quite properly concerned about having any school in this diverse city identified with one particular religious belief or practice.”