Rachid Rokki gave the shock 2010 winners of the second-tier African club competition the lead on 82 minutes only for Pedro 'Fofana' Rodriquez to snatch a 1-1 draw with a goal as the referee checked his watch.
FUS now face a long journey south to Luanda in early May for the second leg against the military club and the odds favour Primeiro reaching the play-off phase where African Champions League third round losers enter the Cup.
Other Moroccan contenders Moghreb Fes and Difaa al-Jadida fared much better and are virtually certain to be among the eight survivors thanks to convincing home victories.
Former Porto striker Tarik Sektioui claimed a 15-minute hat-trick for Moghreb in the 5-1 demolition of Sudanese visitors Al-Khartoum while Zakaria Hadraf was on target twice as Jadida triumphed 3-0 over AS Adema of Madagascar.
Mohammed Chihani nudged Fes into a 16th-minute lead over opponents appearing for the first time this year in the Confederation Cup after receiving a bye and a walkover.
Sektioui opened his account before half-time, converted a penalty just 60 seconds into the second half and struck again on 54 minutes to leave the North Africans sitting pretty on a four-goal cushion.
Mohamed Taib was on target midway through the half for Khartoum but instead of scoring again and keeping the tie alive, Khartoum conceded another goal seven minutes from full-time with Hamza Bourazzouk the marksman.
The hat-trick made former Morocco international Sektioui the leading Confederation Cup scorer this season with five, after a brace in the 4-1 first round triumph over USS Krake from Benin.
Hadraf showed why he is a member of the Moroccan Olympic team with a goal in each half against shock qualifiers Adema before Abderrahim Chakir probably put the tie beyond the Indian Ocean islanders with a stoppage-time penalty goal.
Sunday Emmanuel struck twice in the second half to earn international rookies Sunshine Stars of Nigeria a 2-0 win against Burkina Faso armed forces side USFA in Ijebu Odeh.
Emmanuel broke the deadlock midway through the half, just a couple of minutes after a red card had reduced the Burkinabe to 10 men and snatched the potentially crucial second goal during stoppage time.
Egyptian paramilitary club Harras al-Hodoud are going to find it difficult to reach the group phase a fourth consecutive time having managed only a 2-1 home win over Daring Club Motema Pembe from the Democratic Republic of Congo.
Ahmed Mekki gave Hodoud an early lead only for Tresor Matondo to level four minutes later and the winner came soon after half-time when Ahmed Saied slotted home a penalty awarded for a shove on Ahmed Safi.
Giantkillers Sofapaka of Kenya, who shocked former African champions Ismailia in the second round, fell 2-1 away to Saint Eloi Lupopo in the Democratic Republic of Congo.
But the away goal may prove precious for the Nairobi outfit, who could not field Congolese Patrick Kagogo, Heritier Ndombele and Dodo Kayombo as their refugee status does not permit them to return home.