Good question. The most direct way to measure the expansion history of the Universe is through measurements of distance. If we know how far away something is as a function of time then clearly we can determine the acceleration of the object (I use the term acceleration generally, if the acceleration is negative we could call that deceleration).
For cosmological distances, the best distance measure we have currently are Supernovae Type 1A. These are exploding stars that (we think/hope) explode with the same characteristics for every explosion (so one SN1A explosion is the same way as another). For other SN the nature of the explosion can be quite different, depending on the mass of the star. For type 1A the explosions are the same. This means we know the absolute luminosity (brightness) of these SN and hence by seeing how bright they look to us (since things further away look dimmer the further away they get) these can tell us distances.
The result of the SN data is mainly to show that in recent history the Universe has been accelerating. Current models suggest that the Universe, as you say, was initially decelerating before this. The furthest SN1A that we can see with current instruments lie pretty close to the transition era between acceleration and deceleration, with a few in the deceleration era. With any kind of measurement there are uncertainties involved and therefore you need to do the measurement multiple times to be sure of things. I believe that at present the SN1A results do not directly and unequivocally show evidence for deceleration, since we just don't have enough good measurements far enough away. The next generation of SN instruments (such as space based telescopes) should be able to test this region.
There are however, plenty of other measurement that very strongly speak in favour of the the Universe decelerating in the past. The Cosmic Microwave Background or CMB data strongly favours a model in which deceleration then acceleration occurs. To my mind an even stronger set of evidence is the structure in the Universe. By running simulations of the formation of the large scale structure of the Universe (such as clusters of galaxies, the filaments of material, the empty voids) we find that the structure we see requires a decelerating era to form in. Accelerating slows down the rate at which material can clump together, while deceleration increases it. If the Universe was always accelerating the Universe would be much smoother, without so many galaxies etc. Some people suggest that the Universe has never accelerated or decelerated, that is simply coasts along at a constant rate. Again, the structure in the Universe says that this is not true, we really do need an early decelerating era to seed the structures in the Universe.
So most of the evidence is indirect in a sense, and requires the calculation of the predictions of models, rather than direct measurement. You could argue though that science is always about the predictions of models and is never really 'direct' anyway. That being said the interpretation of cosmological data is very much dependent on the model used to describe the Universe, which could always be wrong. I'm not suggesting our current model is wrong, in fact it works incredibly well, but there is always the possibility that we need to keep in mind.
I hope that helps!