Alexander Booth and Ian Hepworth were 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.
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Reacting to the sentence, Booth's father Chris, who was later seen in tears, said "I'll fight it" and "miscarriage".
Before being dealt with, Booth told the court: "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."
Booth was accused of throwing a plastic bottle at the police during the trouble.
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.
Hepworth was accused of throwing a bottle at the police and then walking forward to pick up a second bottle.
He claimed he could not remember what had happened.
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.
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.
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 Marseille have let their country down.
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 26 feet over a barrier from a promenade on to a hard pebble beach in the south coast city on Monday morning, 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."
Speaking after the court hearing, Booth's father insisted his son was innocent.
Chris Booth said: "It's the lowest of the low. I feel angry, furious, let down.
"Along with my brother we came across to go to the fanzones. On the day, we got the train here from our campsite.
"It started to get rowdy in the Old Port. We had been tear gassed a few times. We moved back to get out the way of things.
"This is when he is supposed to have thrown the plastic glass but my brother said there's no way he threw it.
"All I can think is they said to him if you admit to this you will get out.
"He's been in a solitary cell for 48 hours, still in the same clothes. I have not been able to speak to him or see him.
"I think he is being made a scapegoat of. We are all very respectable people.
"I have witnessed so much violence and hooliganism during these two days.
"Alex did get angry and gobby after he was pepper sprayed but we were walking to the stadium and a police officer pointed at him and he was taken off."
Three more England fans have been jailed for their part in the violence.
Ashley Kelly, 26, from Birmingham, was imprisoned for three months and given a two-year ban from France for throwing seven bottles outside the stadium.
The court heard the construction worker is a single father who lives with his parents.
Paul Jackson, 21, from Halifax, received one month in jail and a two-year ban after he threw bottles at police and supporters on Saturday.
Lee Phillips, 23, from Taunton, was also jailed for one month and given a two-year ban for throwing bottles at a woman, who also threw some back.
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