After two fine away wins, Peterhead failed to make it a third victory and keep the pressure on leaders Stirling Albion.
Two second half goals by the visitors were enough to take all three points in a game where the Blue Toon created little then contrived to miss an open goal with the match all square.
Peterhead were missing several players through injury, Marc Lawrence, Jordan Brown, Nicky Riley and Paul Cairney all absent although Simon Ferry returned to the starting line up.
The visitors broke clear before the game was two minutes old, but Aaron Murrell blazed his shot high and wide.
Peterhead struggled to make any headway against a resolute Berwick backline and it was they who looked the more dangerous when they ventured forward.
Indeed they had the best chance after 28 minutes and it was Murrell again, this time at the back post latching on to a deep cross and it took a double save by home keeper Greg Fleming to keep the score line blank.
Three minutes before the break the Blue Toon finally posed a threat, a header from defender Mason Robertson that hit the crossbar before dropping towards the goal line then cleared.
On the hour Peterhead had one of those misses that looked harder to execute than score.
Jamie Stevenson threaded a pass through to Aidan McIlnuff on the left side of the penalty area.
His square pass found Jack Leitch but he somehow managed to shoot over from a couple of yards out.
Five minutes later a delicate shot from the right side of the area aimed at the far corner by Jamie Stevenson looked like a goal until Rangers keeper Bobby McCrorie dived full length to his right to miraculously turn the ball away.
Those misses came back to haunt Peterhead as Berwick snatched the lead after 72 minutes.
A Chris McDonald free kick 30 yards out went to the back post where full back Oliver Fleming sidefooted in a not undeserved opener.
In the 83rd minute it was all over, Michael McKenna getting on the end of a ball forward from midfield after a corner kick for the home side broke down before rounding keeper Fleming and scoring via the underside of the crossbar.
The result sees Peterhead drop down to fourth in the table and fall six points behind league leaders Stirling Albion.
The gap could have been even larger had the Binos not been held to a 2-2 draw at the weekend against Elgin City.
Stenny have moved in to second after their 3-0 win over Edinburgh City, a result which saw City manager Gary Jardine depart his role making Blue Toon boss Jim McInally the longest serving manager in the SPFL.
Montrose climbed to third with victory over Clyde.
Peterhead now have a two week break from league duties as they travel to face Championship struggelers Inverness Caley Thistle in the Irn-Bru Challenge Cup this Saturday before welcoming amateurs Colville Park to Balmoor the following weekend, Saturday October 14, in the second round of the Scottish Cup.