It was a good day for the leading Irish players as Paul Dunne too carded a 65, taking him to 13 under par for the tournament, only four shots off the leaders.
Fleetwood's back nine included a 25-feet putt on the par-3 15th for birdie and a 50-feet birdie putt on the 16th.
The four-time major victor has had a number of near misses on previous appearances in the UAE capital - he finished runner-up in 2011, 2012, 2014 and 2015, as well as coming third in 2016 - and is keen to finally lift the trophy in his first competitive start since October.
Fleetwood began the week singing the praises of playing partners McIlroy and world No 1 Johnson - and went on to outscore both of them over 36 holes.
"As for me, I'm obviously disappointed, but I didn't really know what to expect after the injury". I wanted to do the right things, and whenever you win it is validation that you can do it. So keeping a hold of it for another year is very nice.
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With only 14 goals scored all season, Liverpool should have little to worry about in terms of a threat on their net. Either way, the Reds should have too much for their Welsh opponents, just as they did in the reverse fixture.
"I've put in a lot of work, I wanted to prepare for this year like I didn't win the Race to Dubai", Fleetwood told Sky Sports Golf. "My game is in really good shape and I saw some really, really positive signs". He hit it really nicely, had control of his ball", remarked Fleetwood of the Northern Irishman, adding: "I think as golfers, whenever you've had a long period off, you always sort of plan for a bit of rust. When I holed putts like I did on 15 and 16 I knew it was going to be my day. My iron play has been poor relative to the standards that I have.
"The challenge is to build on that, and I've made the ideal start". And everything we've done since then was to make sure that we kept progressing, kept improving.
Tommy Fleetwood is getting good at this winning lark.
"He looked great", said Fleetwood, who played the first two rounds with McIlroy.
The 2017 Race to Dubai victor missed last year's event at Dundonald Links, having played in the tournament five seasons in a row prior to that and finishing tenth behind Rickie Fowler when it was held for the first time at Gullane in 2015. This week he has defended his title.