The commission, appointed by the English Football League, said junior staff were pressured to carry out the spying with the aim of gaining a sporting advantage over opponents, including Middlesbrough, whom Southampton had beaten in the semi-finals.
Middlesbrough will replace Southampton against Hull City on Saturday in the playoff final, known as the richest game in football due to the riches of the Premier League that await the winner.
"Mr Eckert accepted, as he must, that information such as team selection and injuries is sensitive information which a club would wish to keep private in the build up to a game," the commission wrote in its ruling.
"He also accepted that he had specifically authorised the observations to obtain information about formation and about the availability of a key player."
The commission, which also handed Southampton a four-point penalty for the next season, criticised the way junior staff were used in the spying scheme.
"The way in which junior members of staff were put under pressure to carry out activities which they felt were, at the least, morally wrong," the commission said in its written reasons for the ruling, which the EFL published on Thursday.
"Such staff were in a vulnerable position without job security and with limited ability to object to, or resist the instructions given to them."