Boonen won the previous two solo stages in front of rival Alessandro Petacchi in bunch sprints, and started the Tour of Qatar with his squad's victory in the team time trial.
Qatar's defending champion extends his lead over Dutch team-mate Steven de Jongh to 27 seconds after pulling away in an early 20-man break-away five kilometres into the 139.50-km fourth stage.
T-Mobile's Bernhard Eisel is third in the overall standings at 33 seconds behind Boonen.
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Petacchi, meanwhile, finished in the main peloton about at five minutes and five seconds behind the 22-man lead group.
Eisel finished seventh on the day even on time with Boonen, but helped his cause in the overall classifications collecting five bonus points by finishing first and second in two intermediate sprints.
Thursday's stage five travels 160.5-km through the flat Qatari desert from Al Zubarah to Mesaieed.
Follow LIVE coverage of the Tour of Qatar every day this week at 12:50 CET on Eurosport 2 television.
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