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Tweeny Witches plays with this. A human girl is whisked away to the world of magic, which is divided into the all-female Witches' world that runs on magic and the Warlocks'/Demons' world (the name is "mazoku" which doesn't exactly translate as "warlock" though the licensors beg to differ) which is based on science so extreme it can fabricate anything anyone wants (though it can't necessarily make the real thing).
Also seen to an extent in Gate, where a gate opens and an army from a parallel magic world attacks. Their magic works in our world and our science works in theirs. The main story's centered on the JSDF soldiers sent to demonstrate to the parallel Empire that the attack was a bad idea. Magic's role varies though, since generally the time it takes to cast a spell relative to the spell's firepower makes other methods more practical in general (especially since there aren't that many wizards).
Magic Users Club has a very light-hearted, humorous take on this with a small high school club of mages trying to defeat an extraterrestrial force that's been hovering for years above their city. Most accept the "Bell" since it has shown no aggression, and its probes are not merely docile in their observations, they actually pay attention to traffic and other laws. The club members are pretty much the only ones who think the thing is up to no good, and it really is, and has determined that the magic these people wield is the only thing that's powerful enough to stop them, or at least sufficiently unknown that they couldn't defend properly.
TV Tropes' "Magic Versus Science" and "The Magic Versus Technology War" articles mention a few others, such as Princess Mononoke, as well.
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