Dickey (7-1) turned in his seventh consecutive start without a loss, yielding only three hits while tossing 66 of his 102 pitches for strikes.
The knuckleballing right-hander had fanned a career-high 11 in his previous outing against Pittsburgh and now has 61 for the year.
Tyler Byrdak recorded the final two outs of the eighth inning and Frank Francisco tossed a 1-2-3 ninth for his 13th save as the Mets took three wins in their four-game series against the Padres.
Daniel Murphy got the game's only RBI with a first-inning single.
San Diego's Edinson Volquez (2-5) absorbed the hard-luck loss, issuing a pair of runs on five hits over 5 2/3 frames.