Saints were removed from Saturday’s play-off final against Hull City after admitting to spying on Middlesbrough, Ipswich Town and Oxford United training sessions.
Middlesbrough, who lost 2-1 on aggregate to Southampton in the semi-finals, have now been reinstated pending an appeal hearing.
Club analyst Will Salt was reportedly caught filming Middlesbrough training from behind a tree before later using his debit card at a nearby golf club cafe.
Le Tissier believes the punishment far outweighs the offence.
“It feels like you’ve been put on trial for murder when all you’ve done is stolen a Mars bar from the corner shop,” Le Tissier told The Sun.
“That’s kind of what it feels like to me.”
The former Southampton forward argued that diving for penalties has a greater direct impact on football matches than gathering information about opposition training sessions.
“When you’ve not been touched by an opponent and you go down in the box, that’s blatant cheating,” he said.
“And that is something that will have far more of an impact on a match.”
Southampton’s removal from the play-offs will cost the club access to the Premier League, with promotion estimated to be worth around £215 million.
Le Tissier suggested the punishment effectively amounts to a financial penalty worth around £100 million given the club’s chance of winning promotion.
The Saints had entered the play-offs on a 21-match unbeaten run under manager Tonda Eckert before the scandal emerged.
Le Tissier also questioned whether the EFL had fully considered the wider consequences of its ruling, with Hull’s preparations disrupted and Wrexham reportedly exploring legal avenues should Southampton’s expulsion stand.
“I’m not sure if they thought through all the ramifications,” he said.
“It’s going to be messy.”
The former England international reserved particular sympathy for Southampton supporters and players, many of whom now face losing a Premier League opportunity through circumstances beyond their control.