Thunder needed to win and hope already qualified Western Storm could do them a favour by beating Surrey Stars at the Kia Oval.
But Ecclestone’s four-wicket haul and a highest total of the season, Stars’ five wicket win meant Thunder missed out on Finals Day next Saturday.
But after just one more boundary, Wyatt mistimed a pull straight to Amy Satterthwaite at mid-on to give Ecclestone her first, and skipper Suzie Bates only managed 11 before Satterthwaite pinned her lbw.
Tammy Beaumont had been uncharacteristically subdued but after nailing her textbook reverse sweep she appeared to grew in confidence, she quickly moved to 34 before Katie Cross had her lbw while playing across the line.
Vipers had been keeping well ahead of the run rate but Beaumont’s wicket saw a dip, with Mignon Du Preez bowled off her pads by Ecclestone.
Sara McGlashan and Maia Bouchier added 37 together in 26 balls to nose the advantage back Vipers’ way, with both striking a brutal six down the ground.
The New Zealand born batsman then swept straight to Bolton at deep square-leg before Bouchier was bowled by Ecclestone.
Ecclestone then completed figures of four for 20 by bowling Amelia Kerr.
Vipers needed 13 from the final over, bowled by Satterthwaite but Paige Scholfield was caught at long on before Charlie Dean and Lauren Bell were run out to close the innings and meant the hosts took home the wooden spoon having won the competition in 2016 and finished runners-up last year.
Lancashire captain Dani Hazell had won the toss and decided to set a total on the same wicket which Hampshire had beaten Gloucestershire in the Vitality Blast the previous evening – which proved sticky.
Nicole Bolton and Georgie Boyce laid out the perfect platform for the high total with good, quick, scoring – the duo punishing the bad balls to reach 48 without loss in the powerplay.
But the first ball after the powerplay, Boyce was run out after brilliant work on the long off boundary by Mignon Du Preez.
Bolton continued amassing runs with impressive boundaries over long on and a skip down the track and middled sweep the pick of her 43.
Amy Satterthwaite received a life, when Sara McGlashan put down a stinging chance at extra cover before she was caught on the reverse scoop and Bolton stumped off an Amelia Kerr googly – which took her to a Vipers joint-best 10 scalps in the competition.
From that wicket at the end of the 15th over, it was the Harmanpreet Kaur show.
Kaur got moving by taking 22 off the 17th over, with Kerr slapped for sixes down the ground and over mid-wicket alongside a pair of fours to the extra cover boundary.
The Indian ended up with 44 from 20 balls in a 55-run stand with Ellie Threlkeld – taking the Thunder to 162 for three.