Del Potro had looked in control of the match early in the second set but the world number one dug deep as he so often does, breaking back twice before dismantling a clearly spent Argentine in the decider.
Victory for Djokovic means that he has now won every match of this year’s event as he bids to win only his second end-of-season title since 2008. Because he is undefeated, he stands to win a whopping $1,760,000 should he go on and lift the trophy.
“It’s my first final here in London at the O2 Arena,” said Djokovic afterwards. “I got to the semi finals in 2010 so this is a step further in my career and I’m trying to enjoy this moment it was a big win.
"He was a set and a break up so he was the better player on the court throughout the first stage of the match and I managed to turn it around and play better, so I am very thrilled to be in the finals tomorrow.”
Standing between Djokovic and his first ATP World Tour title is either Andy Murray or Roger Federer, who play the second semi final on Sunday evening.
“I am definitely going to watch the match and luckily I’m in the final but whoever I play it’s going to be a very tough one.
"It’s the last tournament of the year and we are trying to find extra motivation so I am sure they will play another great match and tomorrow another amazing final.”
Having had an extra day to recover from his final round robin match against Tomas Berdych, it was Djokovic who looked the fresher early on forcing two break points in the second game of the match before comfortably holding to love.
But that was as good as it would get for the Serb as uncharacteristic unforced errors began to creep into his game, largely forced through the thunderous hitting of the Argentine.
Del Potro forced a break point of his own in a long seventh game and although Djokovic dug deep to stave off the danger, the ferocity of Del Potro’s hitting always looked likely to prove decisive and the breakthrough came in the ninth game, a brilliant running forehand bringing up two break points.
Only one was required as another huge groundstroke forced yet another unforced error and with it the opening set.
Del Potro continued where he left off at the start of the second set, his strategy to continue to go for his shots paying off, another booming forehand netting him the early break in the third game.
But having staved off two break points in his next service game, Djokovic out-rallied his opponent to crucially break back immediately and he seemed to grow in stature, breaking again in the eighth game before serving out to level at a set all.
It seemed to take the wind out of Del Potro’s sails and having thrown everything at Djokovic the Argentine now seemed a spent force.
A whipped forehand winner forced an early break to love in the third game of the deciding set and, as Del Potro’s body language visibly dropped, so the world number one’s confidence grew and it was now he who was hitting all the winners.
Another forehand winner forced another break in the seventh game and Djokovic served out to love to book his place in Monday’s final, where he will face the winner of defending champion Roger Federer's clash with US Open winner Andy Murray.