Boonen was languishing in about 50th place with three kilometers of the 140km stage to go but teammate Matteo Tossato helped him reach the front.
"I then let the Milram team [of Petacchi] do the work before waiting for the right moment to start my sprint," Boonen said.
The day started off at a blistering pace with the 57km covered in the first hour before attacks started in the middle of stage, which then left Ireland's Paul Healion with a lead of more than seven-minutes with 40km to go till the line.
1. Tom Boonen (Quick Step, Bel) 6hrs, 33mins, 9 secs
2. Alessandro Petacchi (Milram, Ita) at 13secs
3. Steven De Jongh (Quick Step, Ned) at 17secs
Healion was not able to hang on. A strong headwind did him little favours and the peloton swallowed him up to set up a mass sprint for the line.
Boonen however remained sanguine about his victory over rival Petacchi, who has been injured for much of the last year.
"Petacchi had not sprinted for eights months," said Boonen, who added that he himself was already in great condition.
Wednesday's 139km fourth stage sees the riders start at the Camelodrome with a finish at the Doha golf club.