The Serb, looking to become the first man to win six Masters title in a season, briefly lost focus as Swiss Wawrinka, who beat Djokovic in the French Open final, ended his 29-set winning streak to claim the second set.
But the fourth seed, who knocked out Rafa Nadal in a late thriller the night before, was made to pay as he lost the last six games to a relentless Djokovic who can claim an unprecedented third consecutive Bercy crown when he plays Andy Murray in Sunday's final.
Briton Murray beat Spain's David Ferrer 6-4 6-3.
Djokovic was in a class of his own in the first set as Wawrinka made too many made too many unforced errors.
But the Swiss loosened up in the second set as Djokovic failed to contain his frustration.
It was only a minor disruption though for the 10-times grand slam champion who allowed Davis Cup winner Wawrinka a mere nine points in the decider.
"I still felt like I was hitting the ball well (in the second set)," Djokovic told a news conference.
"You know, with this kind of feeling and approach, I got to the third set and played the best set of the tournament so far."
Wawrinka bowed out with a forehand long, and said the quick turnaround after a 1am finish against Nadal had hurt him.
"It was tough the next day to play against Novak, who is very difficult to play in those conditions," said Wawrinka.
"And of course I felt the tiredness. It was extremely tough for me to fight."
DREAM START
British second seed Murray lost his focus at times against Ferrer but had too much guile for the 2012 Bercy champion.
"I managed to shorten a lot of the points. There was some variety in there with the way the points finished, which was pleasing for me," Murray told a news conference.
Murray made a dream start, breaking to love in the first game, but the Spaniard levelled for 3-3 when two Murray unforced errors gave him a break in the sixth game.
In a see-saw opening set, Ferrer set up four more break points in the eighth game but Murray saved them all and stole the serve of the Spaniard who made a string of unforced errors.
The Scot finished a superb exchange at the net with a fine sliced lob to set up two set points and on the first one Ferrer netted a routine backhand.
In typically tenacious fashion Ferrer got straight back down to business and raced to a 3-1 lead in the second set but Murray then reeled off five games in a row.
Murray will guarantee finishing the year second in the ATP world rankings for the first time if he wins the title.
(Reporting by Julien Pretot; Editing by Ken Ferris and Martyn Herman)
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