The two men were detained on the orders of the Police Internal Investigations Unit following an investigation into acts of sexual abuse reportedly carried out at the Qalandiya border crossing, situated between Ramallah and Jerusalem in the West Bank.
One of the suspects is a combat soldier and the other a security analyst from the Military Police.
According to Jaffa Military Court judge Colonel Ihsan Halabi, the Court has “reached the conclusion that there is prima facie evidence” against the two suspects.
He said the charges relate to “the alleged use of authority to commit serious offences against others”, adding there is an “indication that the acts were motivated by racism”.
In addition, the two men are accused of stealing from Palestinians passing through the checkpoint.
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Neither suspect has been named, and at least one of the individuals has firmly denied the accusations.
An Israeli Defence Force (IDF) spokesman said: “An investigation was opened by the Internal Investigation Unit in the IDF, and the suspended soldiers were arrested and brought before the military court.”
Military Advocate General Captain Ariella Segal added: “There are serious suspicions that a number of offences have been committed and there are additional investigators that must be carried out.”
Major Julia Weinschenker, the attorney for one of the suspects, claimed he is “an excellent and valued soldier who serves optimally in a complex and demanding job”.
She said he admits to carrying out theft as a “one-time occurrence”.
However, she added: “The soldier completely rejects the other suspicions and expects the investigation to end in a way that will negate the suspicions.”
Separately, two Israeli border guards, Amjad Ashqar and Stefan Rashad, have been detained by the Police Internal Investigations Unit on suspicion of robbing Palestinians of $5,600 (£4,283) at checkpoints, with at least one crime allegedly taking place at gunpoint.
The thefts reportedly took place this summer over a period of two months.
Violence continues to erupt along the Israel-Palestine border, and an Israeli-American, Ari Fuld, 45, was murdered in the West Bank by a 17-year-old earlier this week.
The West Bank came under Israeli control following the 1967 Six Day War.
It has a population of nearly three million Palestinians and 370,000 Israeli settlers.