Defender Georgi Dzhikiya was in charge of the Spartak Twitter account on Saturday and had already posted several other videos.
The Russian side posted the offending tweet (that at the time of writing is somehow still up) as a caption in a video that featured black players training in the sun - and also included chocolate bar emojis just in case their words weren't conveying the message well enough.
The tweet was published around 0900 GMT and retweeted over 1,400 times, triggering a wave of criticism before it was deleted nearly five hours later.
BC-SOC-Spartak Moscow-Racism, 1st Ld-Writethru, 292Spartak Moscow posts "racist" tweet about its own playersEds: Updates with new Spartak video denying racism, adds background on previous incidents. "We are a friendly family".More news: Tiger Zinda Hai 24th Day Box Office Collection
"The player did not mean to offend anyone, he simply made an unfortunate joke".
Federation Internationale de Football Association president Gianni Infantino insisted racism will not be tolerated during the tournament and said World Cup referees had been given the power to abandon matches should they deem it necessary.
Leonid Mironov, the 19-year-old captain of the Spartak side, was charged with racist behaviour towards Rhian Brewster last month during a UEFA Youth League game against Liverpool.
"It is a reminder, that along with the whole of football, there is significant work to do to eradicate racism of all forms from the sport".More news: Boeing Unveils New Unmanned Cargo Air Vehicle Prototype
Spartak was ordered to close part of its stadium for another Youth League game after UEFA ruled its fans had abused Liverpool striker Bobby Adekanye with monkey chants.
Former Zenit St Petersburg striker Hulk suggested racist incidents could mar the tournament while Manchester City's Yaya Toure warned Russian Federation back in 2013 that black players could even boycott the finals.
Russia, billed to host the FIFA World Cup in June has a long history of racial prejudices and intolerance.More news: African immigrants in Raleigh 'insulted' by Trump's vulgar remarks