The article cited in support of this idea is entitled "ופליגא במשנת הרמב"ם" and can be found in the work כתבים - הרב יוסף קאפח - חלק ב (p.577).
The opening line of the original article is as follows:
A central tenet which was handed down and accepted by the talmudic scholars of Yemen in the name of the geonim, according to what I heard from the mouth of my grandfather of blessed memory [HaRav Yihhyah Qafihh z"l], is that every place where it says in the Talmud "ופליגא דרב פלוני - ufligha de-rav ploni" the opinion of he with whom the gemara argues in this fashion [lit. הנפלג] is not the halakhah, unless the Talmud goes on to explicitly rule otherwise, or gives any other indication that the halakhah is not like the opinion of one disputing.
Rav Qafihh z"l then goes to explain some of the intricacies of how this principle is discussed by those who wrote commentaries on the Mishneh Torah of the Rambam.
He then begins the next paragraph by stating:
The majority of those who learn the gemara in accordance with set principles who make mention of this particular principle connect it to Rav Sa`adyah Gaon zss"l, and there are those who disagree that it originated with RaSa"G and are inclined to connect it to Rav Shemu'el ben Hhofni Gaon zss"l...
Some of the particular sources he mentions that discuss the attribution of this halakhic principle to various geonim are as follows:
- ר"ש אברמסון בספרו "ענינות בספרות הגאונים" עמ' 68
- השד"ח במערכת הכללים כלל כ': ופליגא
- מרן חיד"א בס' יעיר אוזן אות כא
As for the Rambam, Rav Qafihh goes on to cite each of the 84 instances of this phrase found in the gemara and shows how the Rambam holds firmly and consistently to this principle in both halakhah and aggadah within the Mishneh Torah and other writings (see there). So, while the Rambam doesn't explicitly state this principle, he does explicitly hold to it when codifying the halakhah from the sources of Hazal.
Hope this helps. Kol tuv.