Good question. Perhaps it was not a question of how much control Franco had of his border, but how little control Hitler had there. One might speculate that at the time the Jews were fleeing into Spain, Hitler was busy elsewhere, the Eastern front and North Africa?
Was Hitler going to waste armies to patrol all the passes into the Pyrenees from France into Spain, when he had bigger fish to fry?

James Michener chronicles in Iberia , 1968, page 547: that "...Generalissimo Franco is highly regarded by Jews; during the worst days of World War II, when pressures from Hitler were at their heaviest, Franco refused to issue anti-Jewish edicts and instead provided a sanctuary, never violated, for Jews who managed to make it to Spain. Many thousands of Jews owe their lives to Franco, and this is not forgotten."