Yassine Benzia and El Arabi Soudani scored in each half to ensure Algeria will win Group J.
The group winners and the best two runners-up will qualify for the finals.
The loss for Seychelles means they are unable to win the group and only have a very slim chance of winning a best second-placed spot.
The other match in the group sees Lesotho host Ethiopia on Sunday.
Lille's Benzia scored his first goal for Algeria since swapping national allegiances from France earlier this year.
He scored five minutes before half-time as the Seychelles defence failed to deal with a cross and the ball fell at his feet with his back to the goal before swivelling to score.
Soudani doubled the score on hour mark when as he got on the end of a free-kick from Ryad Boudebouz.
That goal means that Soudani, who plays in Croatia for Dinamo Zagreb, is now the joint top-scorer in the 2017 qualifiers along with Burundi's Fiston Abdul Razak.
Boudebouz then swung in a corner that Hicham Belkaroui headed towards goal only for the ball to be cleared off the line by Seychelles.
Algeria now have 13 points from their five matches and cannot be caught by second-placed Ethiopia, who have five.
The Algerians with interim coaches Yazid Mansouri and Nabil Neghiz at the helm won despite playing without several key players.
Sporting Lisbon's Islam Slimani was suspended while English Premier League champion Riyad Mahrez and Porto's Yacine Brahimi were both injured.
Africa's top-ranked nation Algeria clinched their place at the 2017 Africa Cup of Nations finals on Thursday with a 2-0 win in Seychelles.