The Englishman broke though a tight leaderboard with a superb eagle on the par-5 13th hole and ended the day one shot ahead of Spain’s Rafael Cabrera-Bello on 16-under par 200.
Cabrera-Bello, the 2012 champion here, submitted his third straight card of five-under par 67, while England’s Andy Sullivan was third one behind the Spaniard at 202 after a round of 66.
All three players have something to prove in Dubai.
Willett finished second in the Race to Dubai to Rory McIlroy after his brave attempt went down to the wire at last year’s DP World Tour Championship here.
In that same tournament, a McIlroy win had denied Sullivan the title and he finished runner-up.
Cabrera-Bello’s biggest moment of despair of his career came in Dubai when he was leading the DP World Tour Championship by two shots before losing to Henrik Stenson in 2014 when he made a triple bogey on the 16th hole on Sunday.
World number two Rory McIlroy was languishing eight shots behind the leader.
The Northern Irishman was two-over par after a terrible front nine, but then made six birdies on the back nine to finish on 68.
Henrik Stenson, the second best ranked player in the field at number six, was one shot better than McIlroy at nine-under par after a 70.
Three time Dubai Desert Classic champion Ernie Els, who started the day one shot behind overnight leader Cabrera-Bello, struggled all day and for the first time in the history of the tournament, he posted an over-par third-round score of 74.
Willett, who saw his ball miraculously bounce out of water on the opening day, needed no such luck on Saturday.
He hit the ball well, making 14 greens in regulation, but putted even better, needing just 26 putts to complete the round.
The highlight of the round was the eagle three on the 13th hole, where he drained a curling 40-footer putt. That came moments after he had made his only bogey of the last two rounds on the 12th hole.
Willett was delighted with his form and said: "We came off the first obviously bogey in two days on 12, which was playing pretty tricky today.
"So, come off a silly five there and two five-woods, a little bit of a different story to Thursday when we bounced off the rocks. Today, I hit a good one and saw a pretty good line straightaway.
"Played some great golf yesterday and today. Kept the ball under fantastic control with some crosswinds, hit it in there close.
"Did everything right really. A couple hiccups in there today where it could have been a little different, but kept the head on and kept moving forward.”
McIlroy felt the front nine had killed his chances this week. In the last two rounds, he is five-over par for the front nine, and nine-under par for the back.
"I just think I haven’t quite figured out the front nine yet. Obviously, I’ve played the back nine much better," said the two-time Dubai Desert Classic champion.
"There is more chances on the back nine and more opportunities for birdies, but you know, there’s no reason why I shouldn’t be playing better golf on the front nine.
"That’s really what’s cost me this week. I might be just a few shots too far back to make that up tomorrow.
"It's going to be a long shot. I came back from seven shots behind at Wentworth (2014), so it's not out of the realms of possibility, but this is a great field.”
Select third-round scores in the $2.5 million Dubai Desert Classic on Saturday at the par-72 Majlis course of Emirates Golf Club:
200 - Danny Willett (ENG) 70-65-65
201 - Rafael Cabrera-Bello (ESP) 67-67-67
202 - Andy Sullivan (ENG) 70-66-66,
203 - Joost Luiten (NED) 69-67-67
204 - Haydn Porteous (RSA) 72-66-66
205 - Scott Hend (AUS) 71-68-66, Chris Wood (ENG) 68-68-69
206 - Soren Kjeldsen (DEN) 70-70-66, Nathan Holman (AUS) 69-70-67, Brett Rumford (AUS) 67-70-69, Thorbjorn Olesen (DEN) 72-64-70
207 - Joachim B Hansen (SWE) 72-71-64, Mikko Ilonen (FIN) 70-70-67, Bryson DeChambeau (USA) 70-69-68, Byeong-hun An (KOR) 71-67-69, Graeme Storm (ENG) 68-70-69, Richard Bland (ENG) 69-69-69, Henrik Stenson (SWE) 69-68-70, Alvaro Quiros (ESP) 68-69-70, Trevor Fisher Jnr (RSA) 67-68-72
208 - Roope Kakko (FIN) 72-69-67, Alejandro Canizares (ESP) 71-69-68, Tyrrell Hatton (ENG) 70-70-68, Rory McIlroy (NIR) 68-72-68, Bradley Dredge (WAL) 70-70-68, Bernd Wiesberger (AUT) 68-71-69, Johan Carlsson (SWE) 71-67-70
209 - Nicholas Colsaerts (BEL) 73-70-66, Gregory Bourdy (FRA) 72-71-66, George Coetzee (RSA) 72-70-67, Gregory Havret (FRA) 71-70-68, Ross Fisher (ENG) 70-71-68, Ben Evans (ENG) 69-71-69, James Morrison (ENG) 69-70-70, Gary Stal (FRA) 70-68-71, Ernie Els (RSA) 68-67-74