Police spokeswomen Sally de Beer said three hotel staff, the only people apart from the players who had access to the five rooms affected, were arrested for the Tuesday theft, but charges were dropped against one person.
They are suspected of stealing about $2,000 and 720 euro ($882) in cash. The players were out of the hotel at the time, training for the match against South Africa. The money was not recovered.
"The prosecuting authority decided to prosecute two of the arrested women, who were employed as cleaners, and withdraw charges against the third, who was a supervisor," she said.
The hotel in Johannesburg's affluent Hyde Park suburb is to host Slovenia's World Cup squad, due on June 7.
Police said the theft was an isolated incident and could not have been prevented by the authorities, and should not distract from efforts to make the World Cup safe.
In June last year Egypt's soccer team said some players had had their hotel rooms burgled and wallets stolen during the Confederations Cup tournament in South Africa.
(Reporting by Gordon Bell; Editing by Matthew Jones)