The top seed, who had a first-round bye, next faces 13th-seeded American John Isner or Frenchman Gael Monfils for a place in the quarter-finals.
Djokovic, who is in a race with Roger Federer to end the season on top of the rankings, quickly opened a 3-0 lead playing some aggressive tennis at the Bercy arena.
Kohlschreiber pulled a break back but his opponent held firm to bag the opening set with a service winner.
Djokovic then broke in the first game of the second set as the German struggled to focus.
Kohlschreiber produced a series of beautiful backhand winners but could still not manage to unsettle the Serb.
Djokovic, who became a father for the first time last week, wrapped up victory on his first match point.
"It was a very good match considering the fact that I didn't play indoors for a year (since last year's ATP World Tour Finals). I struggled a little bit physically. It was a pretty tough couple of weeks," DJokovic told reporters.
The Paris Masters will decide who travels to London next month for the Tour Finals with Djokovic, Federer, Stanislas Wawrinka and Marin Cilic already qualified.
Czech Tomas Berdych, the fifth seed who currently sits eighth in the Race to London, reached the third round with a 6-4 6-7(3) 6-2 defeat of French wild card Adrian Mannarino.
A Berdych defeat would have ensured Briton Andy Murray qualified for the Tour finals, but the Czech regained his composure after losing a second set tiebreak, and never looked back after a decisive break in the third game of the decider.
(Editing by Tony Jimenez and Toby Davis)
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