The winger damaged his cruciate ligament in the final league game of the season as his team secured a 5-2 victory over Al Sailiya on Saturday to clinch their sixth league title.
Msakni is expected to be on the sidelines for three to four months and will not be able to play a part in the Carthage Eagles’ campaign at Russia.
“Al Duhail player, Youssef Msakni suffered an injury in the cruciate ligament during Al Duhail's match against Al Sailiya at the end of the QNB Stars League,” read a statement on club website.
“Msakni will be absent for three to four months, and with this injury, he ends his season with Al Duhail, and will also be absent from the participating with his national team at the World Cup in Russia which will begin in June.”
The 27-year-old notched 25 goals in 22 league appearances this season to finish as the second top scorer in the Qatari top-flight behind Morocco’s Youssef El-Arabi with 26 goals.
"Thank God for this, but it's just fate to experience the unexpected," Msakni wrote on Instagram.
"Congratulations for the trophy. Sadly this injury has denied me a chance to continue with my club and to play in the World Cup."