Wawrinka's path to victory had been eased by the retirements of world number one Novak Djokovic and Australian prospect Nick Kyrgios in the earlier rounds but the Swiss often toiled against surprise finalist Baghdatis, whom he beat for a sixth successive time.
World number four Wawrinka was gifted the first set by a Baghdatis double fault -- his third of that game alone -- and a tepid second set was notable for not featuring a single break point.
But then followed a 28-point tiebreak in which twice grand slam champion Wawrinka saved five set points before a Baghdatis backhand drifted long to give the Swiss a second title of the year following his victory in Chennai in January.
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"It's been an amazing year. I'm playing my best tennis since a few years now so hopefully I can keep this level," Wawrinka said.
Baghdatis initially played serve and volley with aplomb, while Wawrinka's stinging backhand was lethal from the baseline, but that early assurance proved fleeting as both players made a catalogue of errors.
Wawrinka afforded Baghdatis two break points after whipping a forehand wide and the Cypriot converted following another wayward Swiss forehand for a 3-2 first-set lead.
Wawrinka, who was within two points of suffering opening-round elimination at the Aviation Club, immediately broke back with a crosscourt winner past the advancing Baghdatis, who was seeking a first title since 2010.
The pair were content to trade half-paced shots from the back of the court and when either did up the tempo it usually failed.
World number 57 Baghdatis, serving at 4-5, saved four set points but his serve deserted him again as he conceded the set.
The second set went with serve before an attritional tiebreak in which Baghdatis fluffed chances to square the match and Wawrinka threw his racket in frustration after missing an easy forehand.
"It was a crazy tiebreak," added Wawrinka. "Until 6-6 I was always up with a mini break ... I did two or three quick mistakes. Then it starts to be all about nerves. You try to play simple, aggressive and it was good to finish in two sets."
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