Djokovic had already guaranteed his place in the last four but he has now secured top spot in Group Guga Kuerten with a game to spare.
The Serbian takes on Marin Cilic in a dead rubber tonight with his fate already sealed.
Zverev ensured he goes through in second place as he edged the battle of the big-servers with a 7-6(5), 6-3 victory over Isner.
The German powered his way through the first-set tiebreak before crucially breaking in the eighth game of the second and serving for the set.
Meanwhile, Federer beat Kevin Anderson in straight sets last night to finish first in Group Lleyton Hewitt.
The Swiss star will face Zverev in the afternoon semi-final at 2pm tomorrow.
Meanwhile, Djokovic will play Anderson in the 8pm night session.
The draw sets up a mouthwatering opportunity for Djokovic to face Federer in a blockbuster final.
The pair clashed in the Paris Masters semi-finals a fortnight ago with world No 1 Djokovic coming out on top over three sets.
However, they must first come through their tricky semi-final ties.
And Zverev, who has won two of his five previous meetings with Federer, is hoping to level their head-to-head record.
“We have played so many times against each other in my short career,” Zverev said.
“He is leading with one win I am hoping to try and change that.
“It is going to be a very tough match but I hope I am ready for it.
“I am unbelievably happy to be through to the semi-finals. John is such a tough opponent. The last two matches for him against Cilic and me could have gone either way.
The first set was unbelievably tight. I am just happy to be through. I will prepare myself the best for tomorrow.”