UEFA last month ordered the Italians to play their next two home European matches behind closed doors, starting with Thursday's Europa League last-16 match against Stuttgart, after the club was charged over the setting-off of fireworks, racist behaviour and insufficient organisation during their last-32 match against Borussia Monchengladbach.
The club were also fined 40,000 euros (£35,000).
Lazio's appeal was rejected by UEFA's Appeals Body on Monday, and Lotito said he was not surprised.
"It was a waste of time," he said in a statement on the club's website. "Everything we did to explain ourselves did nothing. The motivations we still do not know...
"Nothing has been served by coming here. There have been four days spent on the appeal, plus expenses, but it is the story of a death foretold."
It is not the first time Lazio fans have fallen foul of European football's governing body, with the club having previously been punished for racism offences in matches against Tottenham and Slovenian side Maribor.
Fenerbahce will also have to play their next home European match in an empty stadium after their appeal of a charge of throwing fireworks in their recent Europa League clash against BATE Borisov was also rejected.
However, the Appeals Body partially accepted Cesar Navas' appeal against the red card he was shown during Rubin Kazan's last-32 second leg against Atletico Madrid, a match the Russians lost 1-0 only to knock out the holders 2-1 on aggregate.
Navas was dismissed for a late lunge on Falcao, but the partial success of his appeal means his ban is now for two games, rather than three, and he will complete it by sitting out the second leg of their tie with Levante on Thursday.