He bowled 4-20 as the Borderers won in an exciting finish as the visitors ran out of overs to make target.
Berwick had elected to bat and made 177 all out in the 33rd over with Elliott Keenan’s 41 the best score before he was trapped lbw by James Martin-Dobson.
Dominic Donaldson, who hit his second century of the season in a massive mid-week victory over First Division Alnwick in the Thomas Wilson League Cup, made 22 before being caught and bowled by Jonny Wallace.
Skipper James Patterson also knocked 22 before being caught and bowled by Ben Litchfield as Berwick struggled to maintain any long-standing partnerships at the crease, with Allendale’s Wallce taking 5-42.
Thompson took the wickets of top-order batsmen John Welch, Oliver Weeks, Wallace and captain Litchfield, with Jordan Woodcock and Declan Mark each taking a wicket each.
As Allendale closed in on target with Jake Reed and impressive 64 not out, Donaldson clean bowled Michael Cunningham and saw Thompson take a catch from James Martin-Dobson, both for ducks, as he bowled 2-15 in his three overs as they restricted the visitors to 167/8 by the final ball of the innings.
Berwick are fourth in the table and go to third-placed Bomarsund this weekend after taking on Rock in the William Birckett Memorial Cup on Wednesday night.
Tillside suffered a seven-wicket defeat at Cowgate Sports in Division Two and are second-bottom of the table.
They were all out for 186 with skipper Joe Bickerton topping the scoring charts with a solid 58 that included ten boundaries.
Cowgate completed their score chase by the 28th over, running up 186/3 with half centuries from Modussa Ali and Waleed Rahman.
Cameron McGregor, Alisdair Skelly and Sean Whitty were the wicket takers for Tillside, who have a tough fixtute against unbeaten leaders GEMS on Saturday.
Wooler suffered a 9-run defeat at local rivals Warenford in the Dr. Tom Barlow Memorial Cup last mid-week, then slipped to a 6-wicket loss at home to Lions in Division Five (North).
Openers Daniel Graham and Laurie Blackburn both scored 60 in Wooler’s total of 179/8 but a 74 from Pragnesh Patel and 58 not out from skipper and wicket keeper Jay Virpuna helped the visitors to their 182-4 winning total.
The Glendale side are away to Blagdon Park.