The goals scored by Surprise Moriri and Josta Dladla in Sudan means a 2-0 or 3-1 victory will be good enough to see Downs into the next round.
The second leg of the tie in South Africa in two weeks time will decide who goes through to the group stages of the Champions League; the loser drops into the Confederation Cup.
Sundowns looked to have silenced the home side at half time as goals from Moriri and Dladla put them into a comfortable 2-1 lead.
But a brace from Nigerian striker Kelechi Osunwa and one each from compatriot Yusuf Muhammed and Muhammed El-Tahir from the spot cost the South Africans heavily.
Former Enyimba star Muhammed was the Man of the Match and was delighted with his honour:
“It was a team effort and Osunwa was clearly on fire,” Yusuf told KickOffNigeria.com.
“I think its one of my best games this season and we can look forward to the second leg without much worry.
“They are not a bad side but we want to go further than we did last season by winning the trophy, we have a good squad and we are determined.
Zimbabwe’s Dynamos caused a major upset by beating holders Etoile du Sahel of Tunisia 1-0 in the first leg Champions League tie yesterday.
The home side won the third round game in Harare thanks to a strike by veteran Desmond Maringwa.
The goal, according to a BBC Sport report, sparked a wild celebration from Maringwa, who is the only remaining member of the Dynamos team which played Etoile on the way to the final of the competition 10 years ago.
Two-time champions Enyimba of Nigeria were also in good form as they thrashed Tunisia's Club Africain 5-1 in Aba.
Ivorian side Asec Mimosas were held to a 0-0 draw by Morocco's Olympique Khouribga in Abidjan.
Platinum Stars who stunned visiting Al-Ahly of Egypt 2-1 at home on Saturday in another first leg encounter will also have an uphill battle when they meet the Egyptians in Cairo.
The Tycoons took the lead against the five-time African champions after 57 minutes with a goal from Koketso Mmotong.
Egypt international Emad Moteab looked to have earned Ahly a draw when he equalised with just eight minutes left on the clock.
But a goal in injury time from Edward Williams gave the South Africans an unlikely win.
It was Ahly’s first game in this year's Champions League campaign after being given byes in the opening two rounds of the competition.
Ahly’s great rivals Zamalek secured a 3-0 home win over InterClube of Angola - enough to give them hope for the return leg.
Former champions JS Kabylie of Algeria were beaten 3-0 away from home at CotonSport. Daouda Kamilou notched two for the Cameroon champions.