Clijsters bounced back from losing her first set of the week to fight off match points in the ninth game of the second set.
The final was delayed for 74 minutes by rain shortly after Sharapova missed a third chance to win the match late in the second set.
The Fleming Clijsters was playing in her first tournament since taking a month off following Wimbledon.
She seemed unfocussed in the first set and hit just five winners and committed 17 unforced errors while double-faulting seven times.
The two-time US Open champion continued to struggle in the second set.
She already was down a break before saving the three match points on her serve in the ninth game as the incoming weather front produced flag-whipping winds, darkened the skies enough to get the lights turned on and produced a downpour that stopped play.
After holding serve following the rain-break, 27-year-old Clijsters broke Sharapova before holding again to take the game into a tiebreak.
She clawed her way back from the 3-0 deficit to take the tiebreak 7-4, and broke Sharapova in the third game of the final set when the Russian double-faulted.
Clijsters failed to win on three title points, but held her nerve in the end to secure her 38th WTA win