Joe Briggs netted the only goal from the edge of the penalty area on 62 minutes after he had cut in from the right.
Lancers had half-chances throughout the game and Owen Callaghan had a late effort from a goalmouth scramble saved by the Pagham keeper.
Whittington said: “I thought we definitely deserved a draw and we were a bit unlucky.
“We just lacked a bit of quality in the final third but Pagham have some of the best strikers in the league, so I was really pleased with how we defended.
“I think that 0-0 would have probably been a fair result.”
Lancing entertain Hassocks in the league on Saturday.
LANCING: Shaw; Fenton, Hardman, Carruthers, Gathern; Coombe, Bant, Waterman, Melia; Callaghan, Richardson. Subs: Shepherd (Richardson 55), Rance (Coombe 70), Sharman, Sidwell, Flack.