Dimitar Berbatov's stunning volley on the stroke of half-time proved to be enough to give Fulham all three points and add to Stoke's problems away from the Britannia Stadium.
Jon Walters saw a second-half penalty saved by Mark Schwarzer, while the Fulham keeper also produced a fine save to keep out Peter Crouch as Stoke were unable to take anything from their trip to Craven Cottage.
"The first half was flat, the only real quality was Berbatov's great strike," Pulis told Sky Sports HD2.
"In the second half we missed an opportunity, missed a penalty - that's been our story away from home. We haven't taken chances when games have been tight.
"It is always a bad time to concede a goal, but we had a great opportunity with the penalty in the second half and there have been a lot of games we have played away from home where games have been tight we have had chances and we have not taken them."
Pulis refused to be drawn on incidents involving Steven Nzonzi and Robert Huth where it appeared both players were fortunate to escape red cards.
Nzonzi, who broke his nose in an earlier clash with Berbatov, caught Bryan Ruiz in the face with a slap, while Huth appeared to aim an elbow at Philippe Senderos at a corner.
Asked about Nzonzi's clash with Ruiz, Pulis said: "I haven't seen what he did and didn't do."
When quizzed on Huth's confrontation with Senderos, Pulis noted; "I didn't see the elbow on Nzonzi and I did not see that either."