Flintoff, the 18-year-old son of England great Andrew Flintoff, cracked a 65-ball century for Lancashire against Somerset in the final round of group games on Tuesday as he registered his first senior professional ton.
However, the teenager was out for 22 from 39 balls versus Durham at Emirates Old Trafford - one of four wickets taken by Afghan leg-spinner Shafiqullah Ghafari - as Lancashire were bundled out for 187 chasing 350 for victory.
- Scorecard: Ben Stokes' Durham beat Lancashire by 162 runs
- Scorecard: Notts Outlaws beat Yorkshire by three wickets
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Quiet day for Stokes but Durham hammer Lancashire
Former England captain Stokes took one wicket, that of opening batter Harry Singh for 11, as he returned figures of 1-32 from four overs after earlier hitting one six in a knock of 11 from nine balls in Durham's 349-8 in Manchester.
Durham - who will now face Middlesex in a semi-final at Radlett on Sunday - saw David Bedingham strike 104 from 89 balls and Ollie Robinson make 76 from 57 deliveries.
The pair shared a fourth-wicket stand of 149 before Robinson's dismissal brought Stokes to the crease.
In reply, only 17-year-old Joe Moores (51 off 42), who stitched a 59-run stand with Flintoff, made a score of note.
Lancashire lost four wickets for 17 runs from 142-4 once Flintoff was dismissed, with Moores eighth out as the hosts were rolled in 36.1 overs.
Notts advance after horror start to run chase
In the other quarter-final, Notts Outlaws recovered from 1-3 inside three overs to complete a chase of 274 against Yorkshire by three wickets with eight balls to spare in York.
Notts' reward is a semi-final away to fellow Midlanders Leicestershire Foxes on Sunday.
The Outlaws were reeling as Ben Coad (5-52) and Lewis Hill (1-60) removed Ben Martindale (1), Freddy McCann (0) and captain Haseeb Hameed (0) early on, before Kyle Verreynne (105 off 123) and Jack Haynes (116no off 99) hit hundreds.
Verreynne put on 54 with George Munsey (25 off 28) for the fourth wicket and then 154 with Haynes, although Verreynne's dismissal in the 41st over with 65 runs needed triggered a wobble of three wickets for four runs as Farhan Ahmed (2) and Olly Stone (0) fell to Coad, leaving Notts tottering on 213-7.
Haynes, though, found excellent support in No 9 Dillon Pennington (22no off 18), who cuffed the winning four having earlier taken 4-49 with his seam bowling, including Yorkshire top-scorer Will Bennison (91), in the hosts' 273-9.
