Shprygin and 19 other fans were moved from a holding centre in Marseille, where Russian fans battled England rivals last weekend, and put on a plane that left Nice for Moscow.
Before leaving, Shprygin sent a final taunt to French authorities, writing “Good-bye amphibians” on his Twitter account along with a photo of French police at the entrance to the jet.
Russian fans have been accused of staging an orchestrated campaign of violence against England supporters around their Euro 2016 match in Marseille last Saturday.
UEFA has said Russia will be kicked out of the European Championship if their fans cause more trouble inside a stadium during the tournament.
French investigators believe the group expelled Saturday includes well-prepared hooligans but they did not have enough evidence to press charges.
Thirty-five people were injured in fighting between Russian and English fans in Marseille. Three Russian fans have been jailed for up to two years and six England fans for up to three months over the troubles.
French prosecutors say they could still launch an attempted murder investigation over two cases of attacks on England fans.
German police said five Russian fans arrested for an attack on three Spanish tourists in Cologne have been taken into custody.
But Russia has protested over the treatment of its supporters, summoning the French ambassador in Moscow. “I truly don't understand how 200 of our fans could beat up several thousand English,” said President Vladimir Putin.
Europe's football governing body started a new hooligan inquiry on Saturday after Croatian fans threw flares on the pitch, halting their country's match against Czech Republic for four minutes.
Croatia's press highlighted the country's shame after more than 10 flares were thrown onto the turf in Saint-Etienne.
UEFA said Croatia was accused of crowd disturbances, racist behaviour, setting off fireworks and throwing objects.
Turkey was also threatened with action over a pitch invasion and flares and fireworks thrown by fans in their country's 3-0 defeat by Spain in Nice on Friday night.
Croatia's coach Ante Cacic described the fans as “sports terrorists” and President Kolinda Grabar-Kitarovic called a special government meeting on hooliganism.
But the Croatian federation, HNS, said it had told UEFA and France about plans to disrupt game.
“Both UEFA and the French police were warned of hooligans' intentions to interrupt it,” a federation statement said.
The HNS official in charge of security, Miroslav Markovic, said the federation had a “tip-off” there would be incidents in the 85th minute of the match, the state-run HINA news agency reported.
The federation also slammed the lack of action by Croatian authorities to tackle the country's hooligan problem.
“The incident in Saint Etienne is indeed the result of this passive attitude of the Croatian state and today we are all hostages of a group of hooligans.”
Ahead of Euro 2016, Croatian police also sent a list of 326 potential troublemakers to France. Croatian fans have a history of hurling flares at games.
A swastika was drawn on a pitch before a Euro qualifier against Italy last year. UEFA fined Hungary 100,000 euros ($113,000) and ordered the national team to play two matches in an empty stadium.
Fighting erupted Saturday in a Hungarian section of the Marseille stadium before the country's match against Iceland.
Fans attacked stewards who had refused to let two groups of fans separated by a security barrier into the same section, witnesses said.
French riot police halted the trouble.