The defending champion was knocked out by the Swiss in a five-set thriller on Tuesday as he was denied the chance to clinch a fifth title in Melbourne.
"He served extremely well from the beginning to the end," Djokovic told reporters. "Every time he was in trouble, he was coming up with big serves.
"He took his opportunities. He deserved this win today. I congratulate him absolutely. There is nothing I can say. I gave it my best. I gave it all.
"I tried to come out as the winner. I tried to fight till the last point as I did in a very similar match we did last year fourth round, same court. But it wasn't to be this time."
Wawrinka's reward for beating Djokovic is a semi-final encounter with Tomas Berdych.