The Barcelona captain was sent off from the substitutes' bench during Brazil's 3-2 defeat to Japan on Saturday, after protesting the goal that gave the Asian side victory. Brazil coach Carlo Ancelotti was also dismissed during the incident.
Although the match was a friendly, Raphinha is expected to serve a one-match suspension and will therefore be unavailable for Tuesday's meeting with Singapore.
Barcelona would prefer the forward to return to Spain rather than remain with the national team for a match he cannot play. However, the Brazilian Football Confederation has indicated that it has no intention of releasing him.
Rodrigo Caetano, the federation's executive coordinator, explained that Raphinha's presence remains important to the group.
“Raphinha will stay with us. It makes no sense to release him, he is one of our leaders,” Caetano said.
The decision is likely to cause further frustration at Barcelona, who were already unhappy about the forward's latest international call-up.
Raphinha suffered an injury during the previous international break, an issue that kept him out of two Barcelona matches. The club had therefore been concerned about the prospect of losing him again so soon after his recovery.
The latest controversy has also come after Raphinha faced criticism in Brazil over his commitment to the national team. The forward became emotional while addressing suggestions that his focus had been on Barcelona rather than representing his country.
“From the first time I wore the national team shirt, I always made my desire to be here very clear. I have never turned my back on the national team; I have always done everything possible to be present,” he said.
His comments underlined his determination to continue representing Brazil, but the situation has now created another disagreement between the national federation and his club.
Raphinha will not be able to feature against Singapore, yet Brazil believe his leadership is valuable enough to justify keeping him with the squad.
For Barcelona, the decision means their captain will remain away despite being suspended, extending a difficult international period for a player whose availability is important to Flick's plans.