Alexander Booth, Ian Hepworth and Paul Jackson were among the first fans to be dealt with after the widespread trouble in the French port city, which left another fan with severe head injuries and Euro 2016 organiser Uefa threatening to ban England and Russia if there is any repeat.
Booth, 20, from Huddersfield, was jailed for two months for throwing a bottle at police and banned from France for two years.
Hepworth, 41, a psychiatric nurse from Sheffield, was given a three month sentence for the same offence and the same ban.
Reacting to the sentence, Booth’s father Chris, who was later seen in tears, said “I’ll fight it” and “miscarriage”.
Booth, still wearing his England shirt, he said it may have looked like it was aimed for the police but it was not.
He said: “I have never had problems with the police, I respect the police very much. I am hard working.”
According to court papers, it was Booth’s 20th birthday on Sunday.
The prosecutor asked the judge to jail him for two months as that would mean the tournament would have finished by the time he was released.
Booth said: “I would like to say sorry to the police and to the people and city of Marseille. This is not like me; I’m not a violent person.
“I love my job and my family, I’ve never been involved in football hooliganism. I was in the wrong place at the wrong time.”
Hepworth claimed he could not remember what had happened.
The prosecutor asked for him to be jailed for three months, saying he knew what he was doing because he ran away afterwards.
Later this afternoon, Jackson, 21, from Halifax, was jailed for a month and banned for two years for throwing bottles at police and supporters on Saturday.
The injured England fan, Andrew Bache, 50, from Portsmouth, was in a critical condition in a French hospital after being beaten round the head by Russians armed with iron bars.
Russian fans also charged at England supporters in the Stade Velodrome after the two teams drew 1-1 on Saturday night.
But Brice Robin, chief Marseille prosecutor, told reporters that no Russian fans had been arrested in connection with the violence.
Mr Robin said about 150 Russian hooligans had been involved in the trouble, describing them as “hyper violent” and “hyper rapid”.
But just two Russian fans had been arrested, both for a pitch invasion, he said.
Mr Robin said officials had been unable to stop the Russian thugs as they had arrived in the city by train.
A total of six England fans have been charged over the trouble, including a 16-year-old accused of throwing bottles during the chaotic scenes.
Home Secretary Theresa May said England fans involved in the “indefensible” violence in Marseilles have let their country down.
And England manager Roy Hodgson and captain Wayne Rooney have appealed directly to fans to “stay out of trouble” following Uefa’s threat to expel the team from Euro 2016.
The pair recorded a video, shared by the Football Association on Twitter, in which Hodgson asked fans to ensure that Uefa’s threats to dismiss England and Russia “are never carried out”.
Rooney asked those without tickets for games not to travel.
Uefa branded the behaviour of both England and Russia fans before and after the game ‘’unacceptable’’ and said it would not hesitate to impose additional sanctions.
The tournament organiser also opened disciplinary proceedings against the Russian Football Union for alleged crowd disturbances, racist behaviour and the setting-off of fireworks by its fans during the game.
Meanwhile, a Northern Ireland football fan died after a fall in Nice following the team’s 1-0 defeat by Poland.
Darren Rodgers, 25, from Ballymena, Co Antrim, toppled 26ft (8m) over a barrier from a promenade on to a hard pebble beach in the south coast city at around 2am on Monday, police said.
Asked whether David Cameron was concerned that England could be expelled from Euro 2016 over hooliganism, the Prime Minister’s official spokeswoman said: “The Government is deeply concerned by the violence in Marseille at the weekend, including the reports of fans being attacked by rival supporters.
“We welcome Uefa’s decision to launch an investigation into the violence and we will look at how we can support that while engaging with our European partners.”