Peter Tatchell was detained near the statue of Marshal Zhukov in a public square which was busy with football fans ahead of the first game of the World Cup, while holding a poster attacking Russian president Vladimir Putin.
About half an hour into the first half, Russia's scoring midfielder Alan Dzagoyev boosted off for an offensive rush on the goal of the opponents, but fell down, obviously pulling a muscle.
Minutes before Saudi Arabia kicked off the tournament against host nation Russia, Putin said: "I congratulate all of you at the start of the most important championship in the world".
12 minutes into the game, Yury struck his first-ever global goal and also the first in the 21st edition of the quadrennial worldwide football tournament.
The teams continued testing each other in the second half, although Russian Federation was still dominant in ball possession, just like in the previous 45-minuter.
The opening goal came soon after, as Saudi Arabia failed to clear a corner and a curling cross in from the left by Golovin picked out an unmarked Gazinsky to head low into the far corner.
Artyom Dzyuba made an instant impact off the bench to make it 3-0 in the 71st with a header off Golovin's cross.
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The 2018 FIFA World Cup gets under way on Thursday as hosts Russian Federation take on Saudi Arabia at Moscow's Luzhniki Stadium. With the tournament under three days away, Russian Federation will kick off the festivities against Saudi Arabia in the opener.
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Agapov said security staff had no problem with the flag but he did receive abuse from another spectator outside the stadium, who said "I don't want that kind of world".
After a lavish opening ceremony and with President Vladimir Putin watching on, Yuri Gazinsky put Russian Federation ahead with a header off Alexander Golovin's cross in the 12th minute.
Earlier, British pop star Robbie Williams caused a stir during his performance at the opening ceremony by making an obscene gesture to a camera.
Morocco vs. Iran isn't much more attractive than Russian Federation vs. Saudi Arabia. Egypt and Uruguay play Friday in Yekaterinburg.
But if you want to track the tournament through the groups all the way to the final on July 15 you can download Express Sport's World Cup wall chart. They are representing six continents of the world.
Preceding the opening game is the opening ceremony which will give us insight to Russia's entertainment and culture heritage.
Following his release a short time after his arrest, Mr Tatchell tweeted he had been, "charged with violating Federal Law 54 & Presidential Decree 202, which prohibit all protests near the Kremlin & during World Cup".