Murray required a medical time-out at the end of the third set to treat a nasty-looking blister and he went on to lose the next two as the Serb claimed his third successive Melbourne crown with a 6-7 (2/7), 7-6 (7/3), 6-3, 6-2 success.
The Scot put the injury down to wear and tear and felt missing the opportunity to hammer home his superiority at the start of the second set was more damaging to his hopes of recording back-to-back Grand Slam triumphs.
Of the toe, he said: "It's just a pretty large blister. You get them – it happens.
"It was just a bit sore when I was running around. It's not like pulling a calf muscle or something. It just hurts when you run, but it's not something which stops you from playing.
"About 90% of the players on tour will have played this tournament with some sort of blister or problem. It had no bearing on the result."
More frustrating for the world No.3 was his inability to take one of three break points immediately after edging the opening set.
"At this level it can come down to a few points here and there," he added.
"My biggest chance probably came at the start of the second set but I didn't quite take it.
"When Novak had his chance at the end of the third he got his."
Djokovic added: "I knew it was going to be physically demanding, so I needed to hang in there.
"There were a few turning points in the match. Maybe one of them was the second game of the second set when I was 0-40 against the breeze.
"He missed a few shots and I managed to get a crucial hold.
"After that I felt mentally a little bit lighter and confident on the court than I had done in the first hour.
"I needed to be the one who dictated the play and I'm really glad that I played my best."