Indy's goal, and the goal in the story, was to gain control of the Ark of the Covenant and prevent the Nazis from using it either as a weapon or for propaganda. While he is thwarted in this at almost every point in the movie, and, up until the last few minutes, everything he does is undone by the Nazis or Belloq, let's look at what happens after the climax of the story.
After Belloq opens the Ark and unleashes climatic and catastrophic events, Indy and Marian are spared (because they are innately good or because they closed their eyes, or some other reason we never learn). At that point Belloq and all the Nazis with him are gone. But Indy and Marian are still on an island with a German submarine base. Supposedly there would still be members of the submarine crew and the base crew who were not with Belloq and were manning the base and the sub.
We don't know if it was easy or difficult, but Indy is able to take the Ark from where it was, successfully transport it back across the desert, and still arrange to get it back to the United States successfully. At the end we see the Ark in a warehouse in the US (or some English speaking nation), out of hands of the Nazis and in storage.
So up through the climax, Indy had no effect at all, but after that, we have evidence he did achieve his goal and, ultimately, keep the Ark out of Nazi reach and control. We don't see how he did it and it could have been something as simple as signalling an Allied ship to get transportation off the island or as difficult as disabling the Nazi base and commandeering the sub and taking it, with only Marian's help, back to Allied territory.