Alassana Jatta will not be able to play in the first leg of match at the London Stadium on Thursday due to English entry rules for non-EU citizens after Brexit, the Danish club said on Wednesday.
Nigerian winger Ibrahim Said has also been affected by the rule.
“We have tried everything, and have been in close contact with DBU (Danish football association), Uefa, the two embassies and another foreign club which has been in a similar situation,” Viborg said in a statement.
“But unfortunately it has proved to be impossible, as there is a processing time of several weeks and the match was only finally scheduled a week ago.”
Viborg qualified for the playoff round after coming through the qualifying rounds in July and August.
“It’s a shame from a sporting point of view as both players would have had a role in the match,” said Jesper Fredberg, the club’s sporting director. “But it’s even more of a shame from a human point of view that these two are missing out on this great experience.”
The second leg will take place in Denmark on Thursday 25 August, with the winners on aggregate progressing to the competition’s group stage.