A 63rd minute penalty from Baseem Morsi of Zamalek gave the hosts the victory which eliminates Enyimba.
Mamelodi Sundowns of South Africa have already won the group thanks to three consecutive victories.
Five-time African champions Zamalek are second, three points adrift, having played a game more.
Enyimba are bottom of the three-team group having lost all three of their matches.
In Group A, record eight-time winners Al Ahly went out of the African Champions League after their 2-2 draw with Zesco United and Wydad Casablanca ‘s 2-1 win over ASEC Mimosas.
Those results mean that Wydad and Zesco United advance to the semi-finals.
Wydad Casablanca, coached by Wales-born former Real Madrid manager John Toshack, had to work hard for their win and overcome inspired goalkeeping by ASEC Mimosa’s Kouakou Koffi.
Wydad missed a penalty on 29 minutes when Koffi saved from Reda Hajhouj.
But just before the hour Ondama set up Abdeladim Khadrouf, who slotted home.
Yannick Zakri equalised for the visitors nine minutes later with a low shot and Koffi made a series of saves to keep his side on level terms.
With one minute of the match left, a long shot from Salaheddine Saidi was spilled by Koffi, and Ondama slotted in to seal the win for Wydad.
The Casablanca-based club are top of the group on 10 points, with Zesco on eight – the pair cannot be dislodged from the top two spots with one round of games remaining.
Al Ahly’s quest for maximum points failed despite them dominating possession for much of the match against Zesco United in Alexandria.
Zesco, who have booked a first semi-finals appearance, were quick on the counter-attack, and frustrated the Egyptians who are managed by former Tottenham boss Martin Jol.
Kenya’s Jesse Were took advantage of slack marking to nod the Zambians into a sixth-minute lead with Rami Rabia levelling on the half hour.
Were struck again five minutes later, hitting the ball across goalkeeper Ahmed Adel into the far corner.
Veteran striker Emad Meteb was brought on in the second half and snatched an 85th-minute equaliser for the Egyptians.
His penalty area bicycle kick deflected off Kenyan David Owino, leaving goalkeeper Jacob Banda stranded.