The radio chips track attendance, which in turn helps secure school funding.
But Andrea Hernandez, 15, stopped wearing the badge on religious grounds, saying it was the "mark of the beast".
After John Jay High School suspended her, she went to court and won a temporary injunction to continue her studies at the school, without the tag.
The federal court ruling overturned that, saying if she was to stay at the school, she would be required to wear the badge. Otherwise, she would have to transfer to a new school.
The new identification policy at the Northside Independent School District (NISD) in San Antonio, Texas, began at the start of the 2012 school year.
John Jay High School is one of two schools piloting the programme, which eventually aims to equip all student badges across the district's 112 schools with radio-frequency identification (RFID) chips.
The badges reveal each student's location on their campus, giving the district more precise information on attendance.
The daily average of the attendance is related to how much funding each school receives.
But Miss Hernandez said the badge was the "mark of the beast", as described in chapter 13 of the Book of Revelation in the Bible.