The Australian batter also ended on the losing side as her London Spirit team lost by six wickets to last year's runners-up Southern Brave on Friday.
At one stage Mooney looked like she would score the first century in the competition, which has just embarked on its second year, but needing to hit the last ball of the innings for six she managed only two.
The left-hander's shot placement in front of a crowd of around 9,000 at Hampshire's Ageas Bowl was superb, toying with the field as she stroked 16 fours and a six. Her cover-driving had Sri Lankan legend Kumar Sangakkara, on commentary, purring with appreciation.
Southern Brave captain Anya Shrubsole said: "Credit to Beth Mooney, she was outstanding. As a captain and bowler she makes you feel like you haven't got a clue about where to put your fielders."
Mooney's unbeaten 97 off 55 balls was the mainstay of Spirit's 4-155 off their 100 balls with only New Zealand's Amelia Kerr (37 off 27) also reaching double figures.
Kerr was one of three wickets claimed by Amanda-Jade Wellington (3-30 off 20 balls) but Brave's other Australian bowler Molly Strano was 0-33 off her 20.
The total looked competitive, especially as Australia's Tahlia McGrath was absent having been suffering from illness.
But despite tight bowling by another Aussie, Megan Schutt (0-22 off 20), Brave won with six balls to spare.
England's Danni Wyatt smacked 65 off 34 to launch the run-chase before being run out by a direct hit from Kerr after being called for a sharp single by Sophie Dunkley. Her England team-mate made amends by batting through to the end for an unbeaten 34 (off 24).
The 17-year-old Freya Kemp wrapped up victory with 14 from six balls, starting and finishing with a six.
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