Mazembe - who won the home leg of their play-off 2-0 last weekend - held off Kabylie's challenge to continue the defence of their crown.
There was a big shock in Abidjan as former African Champions League winners, Asec Mimosas, were knocked out by CF Mounana of Gabon.
Mimosas went into their home leg needing to overturn a 2-1 deficit from the first leg, but despite fielding a side including the likes of Burkina Faso star Aristide Bancé, the match ended 0-0 with Mounana going through 2-1 on aggregate.
Also on Sunday, Platinum Stars of South Africa squeezed past another Ivorian side AS Tanda to progress 5-4 on penalties after their tie had ended 2-2 on aggregate.
The South Africans went into their home leg in Rustenburg trailing 2-0 overall, but fought back to take the tie to spot-kicks and book their place in the group phase.
It was much more straightforward for another South African side, SuperSport United, who overwhelmed Liberia's Barrack Young Controllers 5-0 in Pretoria.
A hat-trick from Jeremy Brockie helped SuperSport United take the tie 6-1 on aggregate.
Sudan's Al Hilal Obeid defeated Ports Authority of the Gambia 3-0 at home to progress 4-1 on aggregate.
Confederation Cup fixtures:
First leg:
Sunday:
Second legs:
Friday:
Saturday:
Sunday:
Also on Sunday, Nigerian side Rivers United secured a 2-0 home win over Rwanda's Rayon Sports in the only remaining first leg of the play-offs.
The match had been delayed due to the commemoration of the Rwanda genocide.
On Saturday, nine teams booked their place in the newly expanded group phase of the Confederation Cup, including Mbabane Swallows, whose 4-3 aggregate win over Congolese side AC Leopards made them the first club from Swaziland to reach the group stage.
CS Sfaxien of Tunisia became the first side to reach this year's Confederation Cup group phase with a victory over Rail Kadiogo on Friday.
The draw for the group phase will be held on will be on 26 April 2017 in Cairo.

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GB's Abbie Brown opened the scoring after just 15 seconds before Fiji's Litia Naiqato finished off a stunning team move to level.
But Alice Richardson and Joanne Watmore gave Team GB a 19-7 half-time lead, and Brown sealed the win with her second.
Australia and Canada will play in the second semi-final on Monday.
Great Britain earlier beat a strong Canada side 22-0 in their final group game.
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And Brown said that Sunday's improvement came because the team had "settled" after feeling nerves on the first day.
"It is an Olympics, the nerves are going to hit," she said.
"We have shown everyone today with Canada and Fiji, we have done ourselves justice."
Britain's semi-final will get underway at 19:00 BST on Monday, with the final following at 23:00.
Day-by-day guide to what's on
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The African Confederation Cup holders, TP Mazembe of the Democratic Republic of Congo, booked their place in the group phase of this year's tournament with a 0-0 draw away to JS Kabylie in Algeria on Sunday.
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Great Britain women will face New Zealand in the semi-finals of the Olympic rugby sevens after beating Fiji 26-7 in the last eight at Rio 2016.