The result, coupled with a 2-0 last 16 first leg loss in North Africa, meant the five-time champions lost 3-1 on aggregate and were demoted to the CAF Confederation Cup.
Malian Salif Coulibaly, one of many foreigners in a multi-national Mazembe side, raised hopes of a second leg comeback by scoring with a bullet header off a first half corner.
It was the sixth goal this season in the premier African club competition for Hajhouj -- one less than leading scorer Mfon Udoh from Enyimba of Nigeria.
Enyimba will join 1992 champions Wydad and six other clubs in the May 24 group draw thanks to a 4-3 penalty shootout win at Etoile Sahel of Tunisia.
In deep trouble after losing the first leg 3-0, Etoile hit back at home to win by an identical score with Hamza Lahmar scoring in the first half and Brazilian Diogo Acosta twice after half-time.
Record eight-time African champions Al Ahly left it late to edge Young Africans of Tanzania 2-1 and qualify after failing to reach the group stage in the past two seasons.
Hossam Ghaly put Ahly ahead early in the second half only for Zimbabwean Donald Ngoma to equalise midway through the half.
Abdallah El Said snatched the goal that won the match and the tie five minutes into stoppage time in Alexandria.
Ahly, who progressed 3-2 on aggregate, are coached by former Tottenham Hotspur and Fulham manager Martin Jol.
Mamelodi Sundowns of South Africa had hopes of reaching the group stage for the first time in 15 years dashed despite winning 2-1 at home against V Club of DR Congo.
Runners-up two seasons ago, V Club advanced on away goals after snatching a
1-0 stoppage-time victory in the first leg.
Kinshasa match winner Kule Mbombo struck again on 39 minutes in Pretoria and Thabo Nthethe levelled from a softly-awarded penalty before half-time.
Tebogo Langerman put Sundowns ahead 15 minutes from time and usually clinical Zimbabwean Khama Billiat wasted a couple of late chances for the hosts.
ASEC Mimosas of the Ivory Coast were another club to secure a group berth despite losing, 2-1 to Al Ahly Tripoli of Libya in Tunisia.
The former champions qualified 3-2 on aggregate having built a two goal lead in Abidjan.
A couple of other former title-holders, Entente Setif of Algeria and Zamalek of Egypt, and Zesco United of Zambia qualified on Tuesday.
Tuesday, 19 April 2016
ES Setif (Algeria) 0-0 El Merreikh (Sudan) (2-2)
MO Bejaia (Algeria) 1-1 Zamalek (Egypt) (0-2)
Zesco (Zambia) 2-1 Stade Malien (Mali) (3-1)
Wednesday, 20 April 2016
Mamelodi Sundowns (South Africa) 2-1 AS Vita (DR Congo) (0-1)
TP Mazembe (DR Congo) 1-1 Wydad (Morocco) (0-2)
Etoile du Sahel (Tunisia) 3-0 (3-4pen) Enyimba (Nigeria) (0-3)
Al Ahly (Egypt) 2-1 Young Africans (Tanzania) (1-1)
Ahly Tripoli (Egypt) 2-1 ASEC Mimosas (Cote d’Ivoire) (0-2)
Qualified teams: ES Setif (Algeria), Zamalek, (Egypt), Zesco (Zambia), AS Vita (DR Congo), Wydad (Morocco), Enyimba (Nigeria), Al Ahly (Egypt), ASEC Mimosas (Cote d'Ivoire)