The tests were carried out after their match against Sudan last Friday, according to a tweet from tunisie-foot.com on Sunday.
This certainly means the duo will not be available for selection on Tuesday.
Both Sassi and Khaoui featured in the 3-0 win over Sudan in Tunis.
Khaoui scored the opener, before Ali Maaloul and Ben Slimane completed the rout at half time.
Sassi was an unused substitute.
The players have since been dropped from the Tunisian squad for the Eagles friendly and have been placed in isolation.
Meanwhile, the Super Eagles players are also expected to undergo Covid-19 tests on Monday (today).