Rahm held a two-shot lead after playing the first 16 holes in five under par and enjoyed a major slice of luck on the 17th when his second shot was heading out of bounds before hitting a spectator.
However, the world number six failed to make the most of his good fortune by pitching to 10 feet and then three-putting for a six and was also just a few feet from driving out of bounds at the last.
After taking a penalty drop another bogey looked on the cards, but Rahm holed from 20 feet for an unlikely par and Willett got up and down from a greenside bunker for a birdie to match his playing partner's 68.
— The European Tour (@EuropeanTour) September 21, 2019
On 15 under par the pair held a three-shot lead over Justin Rose, Shubhankar Sharma and Christiaan Bezuidenhout, with Scotland's Richie Ramsay and Rafa Cabrera Bello two shots further back.
"Man, those last two holes made it feel a lot worse than it really was," Rahm admitted. "I was really in control of my game and playing good.
"It was not the finish I was looking for, I might have lost a bit of focus, looking into the future instead of staying in the present but it doesn't take away from how solidly I played when the wind was bad and when I still had a fourth shot into the last with a six iron and didn't drop a shot."
Rahm was among the players who waited beside the 18th green on Friday as Jose Maria Olazabal completed his 25th and final appearance in the event and the 24-year-old can join Olazabal, Seve Ballesteros, Miguel Angel Jimenez, Ignacio Garrido and Manuel Pinero as a Spanish winner at Wentworth.
The list of Spanish players that waited around to salute a Spanish legend 🇪🇸 pic.twitter.com/MegDtPi391
— The European Tour (@EuropeanTour) September 20, 2019
"A lot of the things I'm doing are dreams come true and time I can join a list like that is pretty unique," Rahm added. "I have a chance tomorrow and am looking forward to it. It would mean a lot."
Willett recovered from a bogey on the first with the aid of six birdies to remain on track for a seventh European Tour title and a first on home soil.
"This is our biggest tournament of the year for us British guys, it's a massive event," Willett said. "I've been here 10 straight years and I love the place. The crowds are amazing.
"I've won all around the world and it would be amazing to polish one off in front of a home crowd. It's going to be a pretty tough battle out there."
With bad weather forecast for Sunday, Rory McIlroy had not abandoned hope of a second remarkable victory after a superb 65 which equalled his lowest score at Wentworth and left him nine shots off the lead.
"I will give it a go for sure and you never know," said 2014 champion McIlroy. "But at the same time I'm a realist. I know I won from seven back five years ago and I feel like that's something that happens maybe once in your career."
Another rare event was enjoyed by England's Ross Fisher, who holed his second shot to the 18th for an albatross to complete a remarkable back nine of 29 and win a BMW i8 Roadster worth £130,000.
Fisher, whose 66 left him a shot ahead of McIlroy on seven under, said: "It was pretty surreal. I think we had 200 (yards) to the front, 225 to the pin, a perfect four iron. I thought I'd pulled it so I looked away and the crowd's reaction told the rest of the story. To win the car is still a bit shocking."