There are a few factors at play here.
First off, "shot practically" is a distinction that is almost meaningless if it's also allowed to include footage enhanced by computers. While the soundstage shots may be minimal (that would include the close-ups of the Mutt/Spalko duel and the canopy shots, yes?), pretty much none of the jungle chase is digitally unmolested even if they did shoot most of it in Hawaii.
That said, I suspect the CGI is less the culprit than Kaminski's much-maligned aesthetic for the film. Your mileage may vary, but to my tastes the whole movie has a shiny, fake look to it, even when there are no effects in sight. The choices of the DP, for me, obliterate the sense of immediacy, which is crucial in an Indy film. Under the best of circumstances, nothing on screen appears tactile. Once effects get involved, we all but enter Sky Captain territory.
The jungle chase simply looks fake, in a general but palpable way. Not all of us may be able to accurately articulate why, but I think this debate about what, specifically, was CGI or not kind of misses the point. The fact that anything which was shot physically appears ILM'd to the audience summarizes the failure of the sequence better than anything I can think of. Perception is reality. Frankly, the fact that Spielberg shot most of the scene in a real jungle makes it even worse.