The Brazilian was prevented from boarding the flight with his team-mateson Monday due to an irregularity in his documentation, but Bayern's director of sport Christian Nerlinger said the issue has now been resolved.
"There were problems between Brazil and Qatar concerning the visa," he said on the Bavarian club's website.
"It has now been cleared up."
Rafinha has therefore missed the first two training sessions in the winter training camp, but he is due to arrive later on Tuesday evening in time for their third session on Wednesday.
And Nerlinger was keen to point out that Rafinha is "not to blame in any way" for the delay.