Celtic fielded a second string side that won 2-0 in the first-leg, with some players involved in the first team that included Mpusani Tani, Thato Lingwati, Ryan De Jongh, Harris Tchilimbou and Siphelele Luthuli.
Siwelele rested the regular players with the MTN8 final against Orlando Pirates next weekend their number one priority.
The South African side had the big advantage of scoring two away goals without reply in the Democratic Republic of Congo courtesy of Menzi Ndwandwe and Tchilimbou, who both scored inside the first eight minutes.
However, Celtic could not find early goals on home soil, as Maniema broke the deadlock nine minutes before the break and went to the break having pulled a goal back on aggregate.
The Congolese side had good start in the second stanza as they doubled their lead seven minutes inside the second stanza and levelled matters on aggregate.
Neither side could get the clinching goal in the closing stages and they went straight to penalties to determine the winner after a 2-2 draw on aggregate.
Celtic won 3-2 in the penalty shoot-out to secure progression to the second preliminary round to play against the winner between Futuro Kings of Equatorial Guinea and Rivers United of Nigeria.