Rubel was denied entry into South Africa as the local authorities had blacklisted a person with the same name and date of birth.
The quick was prevented from boarding the team flight on Saturday but will now be able to join up with the rest of the squad.
"The security clearance of Rubel has arrived and he will be taking the evening flight," said Bangladesh Cricket Board (BCB) media committee chairperson Jalal Yunus.
The BCB convened an emergency board meeting to resolve the issue with the first Test in Potchefstroom starting on Thursday, September 28.
"We have continuously been in contact with Cricket South Africa, who are also in touch with their home ministry," said BCB president Nazmul Hassan.
"We have received the photo and name of another "Rubel Hossain", whose date of birth also matches with the player. But this person is barred from entering South Africa, so we have confirmed to them that it is not the cricketer Rubel Hossain. I think they got confused, but the photos don't match."
Bangladesh are currently engaged in a warm-up game against an Invitational XI in Benoni.