Goals in the first half from Zineddine Belaid, Fares Chaibi and Ibrahim Maza saw a second-string side, with superstar captain Riyad Mahrez rested, register a comfortable victory at the Stade Moula El Hassan, with veteran Emilio Nsue pulling one back for Equatorial Guinea after the break.
Algeria were already confirmed as group winners after beating Burkina Faso on Sunday to set up a last-16 clash with the Democratic Republic of Congo, enabling them to make nine changes for Wednesday's game.
Nsue, 36, had been top scorer at the last Cup of Nations in the Ivory Coast two years ago, but Equatorial Guinea finished last in the group this time around without any points, unable to reprise their giant-killing heroics of the last Cup of Nations.
In Casablanca, Burkina Faso booked second place in Group E with a 2-0 win over Sudan on Wednesday with goals from Lassina Traore and Arsene Kouassi as their opponents squandered a penalty.
Despite their loss, Sudan also progress as one of the four best third-placed teams.
"This is good for all Sudanese," said Sudan coach James Appiah, whose team next face 2021 champions Senegal in the last 16 in Tangier on Saturday.
In Marrakech, defending champions Ivory Coast came from two goals down to beat already eliminated Gabon 3-2 in Group F as teenager Bazoumana Toure's headed winner in added time handed them top spot in the pool.
The Ivorians finished on seven points from their three games, ahead of Cameroon on goal difference after the latter beat third-placed Mozambique 2-1.
Gabon were eliminated after the second match day following successive defeats and were without injured talisman Pierre-Emerick Aubameyang, but first-half goals from Guelor Kanga and Denis Bouanga gave them a 2-0 lead.
Coach Emerse Fae's side pulled a goal back through Jean-Philippe Krasso, then forced an equaliser via Evann Guessand with six minutes remaining, before Toure sealed the win that sets up a round-of-16 clash with Burkina Faso in Marrakech on Tuesday.
In Agadir, Morocco, teenager Christian Kofane announced his arrival on the international stage with a stunning winner as Cameroon came from behind to beat Mozambique 2-1 and finish second in Group F.
The 19-year-old from Bayer Leverkusen was making only his second appearance for the Indomitable Lions, having turned down call-ups earlier this season to concentrate on his first Bundesliga season.
After squandering several early half-chances on Wednesday, Kofane thrashed home a rocket-like effort from the edge of the area in the 55th minute to win the game.
Five-time Cup of Nations winners Cameroon finished with six points but behind holders Ivory Coast on goals scored.
Cameroon next meet South Africa in Rabat on Sunday.
Mozambique, who went through to the last 16 as one of the best four third-placed finishers, play Nigeria in Fes on Monday in their first appearance in the knockout stages of the tournament.
