Riding under clear skies unlike the previous day, Boonen timed his sprint to perfection, winning the 144.5-kilometer (90-mile) stage from Al Thakhira at Madinat Al Shamal in the northern tip of Qatar.
It was Boonen's second stage win this week and his 20th overall in Qatar.
He improved his overall lead against American Tyler Farrar of Garmin-Barrucuda to 31 seconds with two stages to go.
Farrar suffered a puncture that hurt his team, which won the team time trial on Monday. Farrar finished ninth on Wednesday.
Spanish rider Juan Antonio Flecha of Sky Team was third overall, 34 seconds off the pace.
Boonen emerged the fittest of the riders on a day when stage three winner Mark Cavendish of Britain was left behind with nearly 30 kms remaining in the stage.
Boonen, with help from his Omega-Pharma Quick Step team, increased his break to 21 seconds as fellow riders struggled due to strong crosswinds in the open areas near the finish line in Madinat Al Shamal.
With 5 kms to go, Boonen was racing Dutchman Vellers and Swiss star Cancellara. But the tall Belgian - winner in Doha in 2006, 2008 and 2009 - put in a perfect lunge for the finish line.
On Thursday, the riders start from the Camel Race Track and end the 160km stage five at Al Khor Corniche.
Results of the 147.6km fourth stage of the Tour of Qatar between Al Thakira and Madinat Al Shamal on Wednesday:
1. Tom Boonen (BEL), 3hr 03min 14sec, 2. Tom Veelers (NED) same time, 3. Fabian Cancellara (SUI) s.t., 4. Juan Antonio Flecha (ESP) s.t., 5. Gert Steegmans (BEL) at 4sec, 6. Nikolas Maes (BEL) 11, 7. Yoann Offredo (FRA) 14, 8. Bernhard Eisel (AUT) s.t., 9. Tyler Farrar (USA) s.t., 10. Ian Stannard (GBR) 36
Overall classification:
1. Tom Boonen (BEL) 9hr 50min 50sec, 2. Tyler Farrar (USA) at 31sec, 3. Juan Antonio Flecha (ESP) 34, 4. Gert Steegmans (BEL) 36, 5. Bernhard Eisel (AUT) 45, 6. Tom Veelers (NED) 1:00, 7. Fabian Cancellara (SUI) 1:06, 8. Ramunas Navardauska (LTU) 1:09, 9. Aidis Kruopis (LTU) 1:10, 10. Adam Blythe (GBR) 1:14