That is partly right, although in fact certain books of Aristotle himself were banned, at least in theory. I would also say that the idea that Averroist interpretations of Aristotle were popular in Paris at the time is to believe too much the alarmism of the day - in fact there's not much evidence for what we'd think of as classically Averroist views. Even supposedly card-carrying Averroists such as Siger of Brabant seem not to have held the more extreme views attributed to them.
There were actually two quite different incidents. What happened is this. In the early thirteenth century, there was a movement with Neoplatonic and pantheistic tendencies, not unlike the much earlier thought of Eriugena. It was most associated with Amalric of Bène and David of Dinant. We do not know most of what they actually taught. Amalric recanted his views before Pope Innocent III shortly before dying in around 1206, but his disciples, the "Amalricians", continued to make a noise. In 1210, at the council of Paris, Innocent III condemned Amalric, the Amalricians, and the works (though not the person) of David of Dinant. In one of those nice medieval touches, Amalric was dug up and reburied on unconsecrated ground.
David of Dinant was an Aristotelian scholar who translated, and commented on, the very recently discovered works of Aristotle. These texts of his were widely circulated. Since David was regarded as a pantheistic Amalrician, the general view was that Amalricianism and its pernicious ideas were closely bound up with the study of Aristotle. The university of Paris therefore took the opportunity to ban Aristotle's works on natural philosophy from being read in the arts faculty. Note that it was only the newfound natural philosophical works that were banned (and not even named in the decree), not Aristotle's previously known books on logic, which remained core texts. Also it only applied to the arts faculty, which meant that theologians were still free to read them, and as far as I can tell the ban had no discernible effect other than allowing the then-new university of Toulouse, in 1229, to advertise the fact that its students were allowed to read the books that were banned at Paris. I suppose this was rather like competitors of the iPad advertising that they can play Flash.
The later condemnation wasn't about Amalricianism, it was about Averroism, as LightSpectra said. In 1277 Pope John XXI became worried about certain Aristotelian doctrines supposedly being taught in the arts faculty at Paris. These were a whole range of doctrines, including the eternity of the world and the doctrines associated with Averroism such as the doctrine of "double truth", according to which something could be theologically true but philosophically false. These ideas were associated (justly or not) with characters such as Siger of Brabant, but others were associated with more moderate Aristotelians such as the recently deceased Thomas Aquinas. The Pope was worried that these ideas might spread from the arts faculty (which was inevitably a hotbed of radical thought no matter what anyone did, as the failure of the 1210 ban indicated) to the theology faculty (at which point it would matter, because theology faculties are serious). He therefore instructed Etienne Tempier, the bishop of Paris, to investigate. Tempier commissioned a group of scholars, including Henry of Ghent, to examine the problem. They compiled a list of 219 Aristotelian doctrines, and Tempier condemned them later in that same year.
Just a few days later, Robert Kilwardby, the archbishop of Canterbury, issued a statement of his own, listing doctrines that were not to be taught at Oxford. They included Aquinas' doctrine of the unicity of forms, which Kilwardby believed to have heretical implications (this is the notion that a substance has only a single form). This proscription was subsequently repeated by his successor, John Pecham, who was not only a Franciscan (and thus the mortal enemy of all Dominicans, including Aquinas) but had a deepseated allergy to Aristotle. Naturally, the scholars at Oxford ignored these strictures and insisted that archbishops of Canterbury had no right to tell them what they could teach. One of them, a Franciscan named Richard Knapwell, wrote a book arguing that it was consistent with the faith to believe or reject the doctrine of unicity of forms. Pecham responded to this by simply condemning him. Knapwell protested, in response to which Pecham changed the condemnation to refer only to certain propositions drawn from his work, and not to Knapwell personally. Knapwell was still dissatisfied and went to Rome to protest, where Pope Nicholas IV rejected his complaint. However, the Pope never endorsed Pecham's original condemnation of the unicity theory.
(The Dominicans, of course, went completely off the deep end at this insult to their most famous theologian (even though Kilwardby himself was a Dominican) and in 1279 held a council of their own at which they banned anyone from criticising Thomas Aquinas on any grounds. It took until 1914 for a Pope to endorse Aquinas' theory of the unicity of forms, though.)
The important point here is that the 1277 proscriptions at Paris and Oxford alike were of various doctrines associated with Aristotelian thinkers, not books or Aristotle himself, and some of the doctrines condemned were ones that Aristotle himself would not have held (such as the unicity of forms).
