In the previous qualifying round of the secondary African club competition, the Ugandan outfit slashed costs by making a 25-hour bus and ferry journey to Zanzibar.
Travelling by road from Central Africa to Morocco in the north west of the continent was not practical, though, and club president Ben Misagga has hailed the assistance of Museveni.
"I thank President Museveni for coming to our rescue with his financial offer," the official told reporters in Kampala. "We are flying the Ugandan flag in Africa.
"The kindness of the head of state is a massive morale boost and makes us even more determined to achieve a good result in Rabat."
Seventeen of 56 football associations eligible to enter the Confederation Cup this year declined, largely due to financial constraints, and two clubs withdrew after the draw was made. Debutants Villa are the only last 16 team boasting a perfect four-match record after home and away wins over Al Khartoum of Sudan and JKU of Zanzibar.
Midfielder Godfrey Lwesibawa scored twice and five team-mates also contributed to a 7-0 goal record.
After a preliminary round bye, 2010 Confederation Cup winners FUS battled to oust modest UMS Loum of Cameroon 3-2 overall with Mourad Batna scoring the tie clincher.
Villa coach Ibrahim Kirya is unconcerned that the Rabat club are favoured to reach the play-off stage, where CAF Champions League last 16 losers join the competition.
"We will not tremble at all and I believe my team can achieve a respectable away result," he promised.
Azam of Tanzania and Al Ahly Shendy of Sudan, the other East African survivors, enjoy home advantage first against Esperance of Tunisia and Medeama of Ghana respectively.
Ivorian Kipre Tchetche, part of a multi-national Azam squad coached by Briton Stewart Hall, scored the only hat-trick of the previous round in a 7-3 triumph over South African side Wits.
Esperance also struck seven goals in eliminating Renassance of Chad and two came from Taha Yassine Khenissi, who is injured and misses the trip to Dar es Salaam.
Shendy, making a fifth consecutive appearance, should be wary of Abass Mohammed, whose two goals took Medeama past Al Ittihad of Libya.
Winners Hearts of Oak and Asante Kotoko featured in an all-Ghana first Confederation Cup final 12 years ago, but no club from the West African nation has come close to glory since.
North African sides have dominated, winning nine of 11 finals, and there are two each from Algeria, Egypt, Morocco and Tunisia among the 16 survivors.