The Pilgrims were beaten 2-0 at Chorley after conceding twice inside a five-minute spell before the break.
Whitham powered home a 34th minute header and O'Keefe converted from the spot five minutes later following a Marcus Marshall handball.
Chances were few and far between in the early stages, with Gregg Smith rising to power Jason St Juste’s right-wing cross off target, while Paul Jarvis’ free-kick flew too high at the other end.
United, missing six first choice players through injury with two more only deemed fit enough for the bench, struggled to make real headway in the attacking third and subsequently fell behind with 11 minutes of the first half remaining.
The Magpies took the lead when Jarvis wriggled free to cross from the left and WHITHAM peeled off his marker to power home a close-range header.
Matters took a turn for the worse for United when Stephen Jordan’s drive crashed back off Marshall’s arm and O’KEEFE sent Christian Dibble the wrong way from the spot.
Jarvis had a further chance to extend Chorley’s lead before the break, but his dipping drive flew just wide.
United threatened briefly after half-time with Lamin Colley denied by a good Sam Ashton save, but the Pilgrims failed to gather any real momentum.
Marcus Carver missed two gilt-edged chances to extend Chorley’s lead, before Dibble made successive saves to deny O’Keefe (twice) and Carver again as United’s comeback bid fizzled out.
Chorley (3-5-2): Sam Ashton; Scott Leather, Kieran Charnock, Stephen Jordan; Matt Challoner, Josh O’Keefe, Dale Whitham, Jake Cottrell (Adam Blakeman 84), Paul Jarvis (Will Beesley 75); Marcus Carver, Sefton Gonzales (Jason Walker 62). Subs (not used): Andy Teague, Waqas Azam.
Boston (4-4-2): Christian Dibble; Joe Burgess, Ollie Price, Joe Maguire, Courtney Wildin (Cameron Johnson 49); Marcus Marshall (Liam Adams 73), Grant Roberts (Lewis Hilliard 58), Jack McMillan, Jason St Juste; Lamin Colley, Gregg Smith. Subs (not used): Jay Rollins, Michael Emery (gk).
Referee: Will Finnie.
Attendance: 1,009.