In a tight opening set, world number 26 Wawrinka was able to match Djokovic and force the tie-break.
Both players swapped mini-breaks twice before the Serbian found a third to serve out 7-5.
The world number one took control in the second as two breaks gave him the opportunity to clinch the match.
There was still some fight in Wawrinka as the Swiss broke Djokovic for the first time in the set to give himself a slim chance of a recovery.
However, it only delayed the inevitable as Djokovic served out the match 6-4.