Clijsters edged out the Belarusian in a cagey opening set, before losing a dramatic second after being broken in two successive games.
But the Belgian responded with a crushing 6-1 sweep of the third as a weary Azarenka folded, and her strength proved too much.
With maroon and white Qatari flags fluttering above the Khalifa Tennis Complex, conditions were much more comfortable for the players than the oppressive humidity of the first two days.
The early signs were ominous for Azarenka as her serve was ruthlessly broken in just the second game of the match.
Clijsters wavered immediately on her own serve, and a tight opening set ensued after Azarenka had broken straight back to restore parity.
But the number three seed finally grabbed the decisive break to clinch it 6-4 as Azarenka's delivery faltered crucially.
The pair traded breaks of serve at the start of the second set, before repeating the pattern at 5-5.
Azarenka broke for a third time to clinch the set, and served out to take the second 7-5 in a gruelling finale.
The Belarusian cut a weary figure in the final set and was broken twice in succession as Clijsters stamped her authority back on proceedings.
Clijsters sealed the final set 6-1 to clinch victory, the second of her campaign in Doha.
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Yet another see-saw match. Honestly I think this is why I don't watch WTA matches outside of the grand slams anymore.
The excitement factor is not at the same level as the guys, matches like these are case and point.
Nevertheless happy Kim has won another match :). Rooting for her to win the whole thing.