Six players have already qualified for the season-ender in London and victory in Vienna lifted Ferrer to equal seventh in the ATP Race standings with Japan's Kei Nishikori.
Both players lead ninth-placed Frenchman Jo-Wilfried Tsonga by more than 1,000 points with precious few opportunities left for the gap to close, although there is still one Masters 1,000 event still to come in Paris.
"It's been an unbelievable season, winning five titles and it's great to be playing well," Ferrer said.
"I am in a good position for (ATP World Tour Finals in), but I have yet to qualify. Certainly, today I took a big step."
Johnson, ranked 47, took the opening set when a forehand winner allowed him to break the Ferrer serve in the 10th game having been pegged back after forging 3-0 ahead.
But Ferrer hit back to level the match and pounced at 5-5 in the decider when Johnson served a double-fault on break point.
Ferrer then locked the door, sealing the win when Johnson netted after two hours and 14 minutes.
Johnson came mighty close to a first ATP Tour title though, when he reached 30-30 on the Ferrer serve with the Spaniard at 4-5 down in the deciding set.
"He just had a bit more experience," said Johnson. "I had some looks at 5-4 (in the third set), then at 5-5 he played a couple of incredible shots.
"I had an awesome week and am super-proud about how I played. I'm not going to be sad about this week and I look forward to the rest of the year."
Novak Djokovic, Roger Federer, Andy Murray, Stan Wawrinka, Rafa Nadal and Tomas Berdych have already qualified for the Nov. 15-22 season ender in London.
(Reporting by Martyn Herman, editing by Pritha Sarkar)
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