The Dane, who went on to win the title in Fuzhou on Sunday, drew ire when he threw a discarded shirt belonging to Malaysia's Iskandar Zulkarnain Zainuddin on to the court during a break in their semi-final.
Zainuddin took offence and told Malaysian media: "My jersey has the Malaysian national flag. I don't have a problem if you want to disrespect me. But please respect the Jalur Gemilang (Flag of Malaysia) on my shirt."
Irate fans took to social media to criticise Jørgensen, who later issued an apology via Facebook.
"I'm sorry for all the Malaysians I have offended by throwing Iskandar's shirt. Not my meaning to be disrespectful... I have a lot respect for him," Jørgensen wrote.
It did little to placate some fans, with one commenter on Instagram writing: "Pls learn how to respect people dude!"
The row comes after a group of Australians dubbed the "Budgie Nine" were detained for stripping down to swimwear decorated with the Malaysian flag during the country's Formula One Grand Prix last month.
Jørgensen and his Danish teammates are well known for their spirited behaviour on court, with shirtless victory laps and emotional outbursts common at their matches.