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The match should have been played at Ajaccio's own Francois-Coty stadium but French league officials switched it to a neutral venue and behind closed doors as the Corsican club were punished for the violent scenes which plagued their Ligue 2 play-off against Le Havre last week.
On Wednesday, Max-Alain Gradel gave Toulouse the lead with a first-half injury time free kick.
Ajaccio goalkeeper Jean-Louis Leca injured his right shoulder trying to save the shot and was replaced by Riffi Mandanda.
Central defender Christopher Jullien added the second goal in the 51st minute with striker Sanago tucking away a third on the night from a 65th free-kick to give Toulouse a comfortable cushion ahead of Sunday's second leg.
Ajaccio's scheduled play-off against Le Havre had been postponed in surreal scenes on Friday after fans of the Corsican club attacked the visitors' team bus.
Players and officials from Le Havre were subjected to racist abuse, called "shitty French" and, according to videos circulating on social media, sat in terror inside the team bus as it was hit by stones and other projectiles.
Then on Sunday, the rescheduled tie finished 1-1 after 90 minutes, but Ajaccio midfielder Mathieu Coutadeur was sent off in extra time after pushing the referee, who also awarded a penalty, which on-loan Lyon striker Jean-Philippe Mateta scored to put Le Havre 2-1 up.
Mateta was then sent off for the provocative manner in which he celebrated his goal.
Two more players were also dismissed, leaving the sides to complete extra time with nine men each.
Ajaccio's Mady Camara made it 2-2 in the fifth minute of added time in extra time, forcing penalties, and the Corsicans duly won the shoot-out 5-3.
In Ajaccio on Wednesday around 2,000 supporters of the Corsican club watched the game on two giant screens inside the François-Coty stadium.
Coutadeur and Joris Sainati, two of the four players sent off on Sunday, turned up to lend their long distance support.
"I'm sad for me and Ajaccio as they are handicapped a little bit by this and it also handicaps us not seeing them at home tonight," said 33-year-old supporter Moune.
"What happened is unfortunate, but I think the media and everybody realises that this kind of thing happens every weekend at every ground."
