Scores were locked 10-10 for much of the final quarter, and it was anyone's game.
Both sides were visibly tired after long seasons but neither wanted to give the match away.
In the end, it was a 79th minute Rhys Harrold penalty that won it for Clutha, completing an excellent season.
Clutha coach Ben Keach was ''over the moon'' with the win.
''It was the icing on the cake, really,'' he said.
''These boys have been there for four or five years and just couldn't get over. They just showed a fair bit of heart.''
Alexandra opened the scoring with a Rory Campbell penalty and the home side dominated the opening period by holding most of the possession.
However, Clutha scored the first try of the game, prop Dan Groen crashing over to instigate a dominant period before and after halftime.
Clutha led 10-3 at the break but Alexandra finally got its hands on the ball later in the second half and prop Nathan Lyon levelled the scores.
Alexandra had a number of other scoring chances in the half but was thwarted by some fine Clutha cover defence.
The winning play came after a miscued Alexandra chip kick led to a Clutha breakaway before the home side infringed at the resulting ruck about 25m out. Harrold duly obliged and got the South Otago side home.
Alexandra coach Tony Sanders was disappointed but proud of the way his side played and the season overall.
''It was a cracker of a game,'' Sanders said.
''Unfortunately, we were on the wrong end. They [Alexandra] punched above their weight week in and week out and I'm proud of the way the boys played.''
Clutha lock Rym Geary (37) was ''outstanding'' and halfback Jared Edwards was also excellent, especially on defence.
For Alexandra, the centre pairing of Michael Cartmill and Simon Lloyd stood out for the second week in a row and flanker Shane Harrex was also prominent.
Players from both teams will feature for Otago Country against Southland Country in Gore this Saturday.
Country final
The scores
Clutha 13
Dan Groen try; Rhys Harrold con, 2 pen
Alexandra 10
Nathan Lyon try; Rory Campbell con, pen
Halftime: Clutha 10-3.
