Chadian Ezechiel N'Douassel put the visitors ahead midway through the first half at Nyayo Stadium, Dodo Kayombo levelled before half-time and John Barasa and John Onami were on target in the latter stages of a lively match.
Kaduna booked their place by defeating nine-man Entente Setif of Algeria 3-0 in northern Nigeria to avenge a one-goal first leg loss with Jude Aneke bagging a brace and Rabiu Baita scoring the other goal. National call-ups, suspensions and injuries slashed the Setif squad to 13 for the journey to the west of the continent and defender Mohamed Yekhlef and Abdelmoumene Djabou were shown red cards either side of half-time.
Sunshine Stars completed a 'double' for Nigeria by defeating Tripoli-based Al-Ittihad 1-0 in south-western town Ijebu Ode in a tie reduced to a single match because of the Libyan conflict.
Simba of Tanzania built a 1-0 lead in Dar es Salaam over Daring Club Motema Pembe from the Democratic Republic of Congo in the delayed first leg of an encounter set to be completed this month.
Stars and Simba or Pembe will feature in Group B with JS Kabylie of Algeria, who have won the CAF Cup three times, the CAF Champions Cup twice and the African Cup Winners Cup, and Moghreb Fes of Morocco.
Sofapaka shocked Ismailia of Egypt in the second round by overturning a two-goal away defeat and edged vastly more experienced Saint Eloi Lupopo of DR Congo last month to become the first Kenyan qualifiers for the fourth round. But they faced a mammoth task at home to Club after losing 3-0 in Tunis and physically formidable N'Douassel came close several times before rounding goalkeeper George Opiyo and slotting the ball over the line.
That left Sofapaka needing at least five goals to survive and DR Congo-born Kayombo equalised just before half-time by prodding in a Titus Mulama free-kick. Tunisian goalkeeper Sami Nefzi was the busiest footballer on the pitch as Sofapaka bombarded his goalmouth and outstanding veteran Barasa and Onami did score only for the dominant Kenyans to run out of time.
Simba succeeded despite having defender Haruna Shamte sent off early in the second half for fouling Salakiaku Matondo, joint leading scorer with five goals in the Confederation Cup this season. But Pembe, who sacked Belgian coach Nasreddine Nabi this week and replaced him with assistant Andy Futila, failed to take advantage of their numerical superiority and fell to a Hassan Musa goal seven minutes from full time.
Godfrey Oboabona scored from a penalty five minutes into the second half for Sunshine and ensured Nigeria will be the only country with two contenders for a trophy lifted by FUS Rabat of Morocco last year.