The Norwegian time trial champion completed the course in 13-26, 25 seconds faster than runner-up Jos Van Emden (LottoNL-Jumbo).
Previous race leader Mark Cavendish finished seventh, 44 seconds down on his teammate and is now second on GC at 26 seconds.
The third stage of the race was held over a flat 11.4 kilometre circuit consisting of eight tight turns linked by long straights. Lieuwe Westra (Astana), former Dutch time trial champion, set an early benchmark, before being eclipsed by compatriot Jos van Emden, who set a time 13 minutes 51 seconds.
That time stood until Boasson Hagen, who began the day 18 seconds behind Cavendish, set a time of 13-26, enough to lift him from fifth to first place.
Heading off last, Cavendish had his work cut out retaining the race lead but shouldn't be too disappointed with his ride. The Manxman lost the lead to his teammate rather than a rival, and finished in a strong seventh position - which points to good form at the start of a season where he has set himself some ambitious goals.
Cavendish still leads the points classification and sits second on GC. The likelihood of cross winds on tomorrow’s 189km stage between Al Zubarah Fort and Madinat Al Shamal means the general classification is far from decided, though Dimension Data are certainly in a strong position.
Tour of Qatar stage three, Lusail-Lusail (11km TT)
1. Edvald Boasson Hagen (Nor) Dimension Data, 13-26
2. Jos Van Emden (Ned) LottoNL-Jumbo, at 25s
3. Manuel Quinziato (Ita) BMC, at 29s
4. Greg Van Avermaet (Bel), at 32s
5. Dmitriy Gruzdev (Kaz), Astana at 40s
6. Lieuwe Westra (Ned) Astana, at 43s
7. Mark Cavendish (Gbr) Dimension Data, at 44s
8. Jordan Kerby (Aus), Drapac, st
9. Soren Kragh Andersen (Den) Giant-Alpecin, at 45s
10. Daniel Oss (Ita) BMC, at 47s
Tour of Qatar GC after stage three
1. Edvald Boasson Hagen (Nor) Dimension Data, 06-53-35
2. Mark Cavendish (GBr) Dimension Data, at 26s
3. Manuel Quinziato (Ita) BMC, at 32s
4. Greg Van Avermaet (Bel) BMC, at 34s
5. Alexander Kristoff (Nor) Katusha, at 45s
6. Soren Kragh Andersen (Den) Giant-Alpecin, at 48s
7. Sven Erik Bystrom (Nor) Katusha, at 1-02
8. Sam Bennett (Irl) Bora-Argon, at 1-07
9. Viacheslav Kuznetsov (Rus) Katusha, at 1-10
10. Michael Schar (Swi) BMC, at 1-15
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