Three days is the minimum reasonable itinerary for the Pantanal. With wildlife viewing, the longer you spend in an area, the better your chances of seeing animals. Spend the minimum possible time in Cuiabá then a take a slow wildlife-spotting drive out along the Transpantaneira to a lodge. Take a guided hike, and after sunset, go for a spotlight drive on the Transpantaneira to see the night creatures: capybaras, tarantulas, and (with the most incredible of luck) jaguars. I also strongly recommend that you take the time to explore the Pantanal as it was meant to be seen, on the back of a horse. Canoeing one of the North Pantanal's small rivers is a great way to spot monkeys and giant river otters.
After exploring the Pantanal, consider a 1-day or overnight trip to the Chapada dos Guimarães, the highlands to the north of Cuiabá. The beautiful red-rock formations, plateaus, and canyons offer excellent hiking and fabulous views, great waterfalls and swimming holes, and some excellent bird life, including red macaws.
Driving the Transpantaneira -- There are a couple of ironies about the Transpantaneira. Though the name implies that the road traverses the entire Pantanal, the highway stops in Porto Jofre, 144km (89 miles) from where it began, and at least that far from the opposite edge of the Pantanal. The other irony is that the project, which if completed would likely have destroyed the Pantanal (by skewing the ecosystem's drainage pattern), has instead, in its unfinished state, become one of the great wildlife-viewing areas of the world. Ditches on either side of the roadbed have become favorite feeding grounds for kingfishers, capybara, egrets, jabiru storks, giant river otters, and caiman by the dozen. Spend but a day on the Transpantaneira, and you'll see more wildlife than you'd see in a week in the Amazon.
Note: This information was accurate when it was published, but can change without notice. Please be sure to confirm all rates and details directly with the companies in question before planning your trip.