Wawrinka, seeded second, had been two points from defeat in the Dubai tournament's first round to Sergiy Stakhovsky of Ukraine.
This is the third time that Wawrinka has played in Dubai. In his previous two visits, the Swiss star never won a match.
The victory is Wawrinka's second title of the year. He won a third consecutive Chennai title last month and has won the last nine finals he's played, including the 2014 Australian Open and 2015 French Open. He last lost a final in 2013.
Baghdatis, who was unseeded, has now lost his last seven finals.
Wawrinka, who has beaten Baghdatis all six times they've played, broke serve on a fifth set point in the 10th game to close out the first set. Baghdatis double-faulted three times in that game, including the final point.
There were no break points in the 12 games of the second set.
Wawrinka initially led 4-1 in the tiebreaker, and saved four set points to win on his fourth match point on a Bagdhatis backhand error.