Brazilian Lucas scored in the 57th minute while Sweden forward Ibrahimovic struck late on as PSG finished second in the table with 13 points from six games, behind Real Madrid (16) who crushed Malmo 8-0 in the Spanish capital.
Shakhtar wasted a few scoring opportunities on Tuesday as they ended in third place on three points, ahead of Malmo on goal difference, to qualify for the Europa League.
PSG coach Laurent Blanc rested several players with captain Thiago Silva and midfielder Marco Verratti not included in the squad and Edinson Cavani, Thiago Motta and Angel Di Maria starting on the bench.
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Unbeaten at home in a Champions League group game since 2004, the Ligue 1 title holders had a good opportunity early on when Ibrahimovic intercepted a poor pass by keeper Anton Kanibolotskiy but his lob flew just over the bar.
Lucas opened the scoring in the second half with a low cross-shot from just outside the box following an impressive run through midfield by Blaise Matuidi.
Ibrahimovic wrapped up victory with another low drive in the 86th minute.
(Reporting by Julien Pretot; Editing by Tony Jimenez)
