The decision means Greek team PAOK Salonika, beaten by Metalist in the previous qualifying round, will face Germany's Schalke 04 in the two-legged playoff tie later this month as ruled by European governing body UEFA earlier this week.
CAS said it had considered written submissions from UEFA and PAOK along with "the urgent request for provisional measures filed by FC Metalist Kharkiv."
"After having considered the parties' submissions, the deputy president of the appeals arbitration division decided to dismiss FC Metalist's request," said CAS.
"Consequently, the UEFA decision remains in force, which means that FC Metalist Kharkiv is excluded from the 2013/2014 UEFA competitions.
Metalist, last season's Ukrainian league runners-up, were barred by UEFA on Tuesday over their involvement in a domestic match-fixing case in 2008.
"UEFA has welcomed the Court of Arbitration for Sport's decision to reject the application for provisional measures made by FC Metalist Kharkiv after the club were banned from UEFA competitions," said UEFA in a statement.
Last month, Turkish club Fenerbahce, banned from European competition for two years for their involvement in a domestic match-fixing case, were provisionally reinstated to the
Champions League by CAS pending an appeal. They beat Salzburg in the third qualifying round and will face Arsenal in the playoff round.