We report the results of the Swift and XMM observations of the Swift-discovered long Gamma-Ray Burst GRB 060729 ($T_{90}$=115s). The afterglow of this burst was exceptionally bright in X-rays as well as at UV/Optical wavelengths showing an unusually long slow decay phase ($alpha$=0.14plm0.02) suggesting a larger energy injection phase at early times than in other bursts. The X-ray light curve displays a break at about 60 ks after the burst. The X-ray decay slope after the break is $alpha$=1.29plm0.03. Up to 125 days after the burst we do not detect a jet break, suggesting that the jet opening angle is larger than 28 degrees. In the first 2 minutes after the burst (rest frame) the X-ray spectrum of the burst changed dramatically from a hard X-ray spectrum to a very soft one. We find that the X-ray spectra at this early phase can all be fitted by an absorbed single power law model or alternatively by a blackbody plus power law model. The power law fits show that the X-ray spectrum becomes steeper while the absorption column density decreases. In Swifts UV/Optical telescope the afterglow was clearly detected up to 9 days after the burst in all 6 filters and even longer in some of the UV filters with the latest detection in the UVW1 31 days after the burst. A break at about 50 ks is clearly detected in all 6 UVOT filters from a shallow decay slope of about 0.3 and a steeper decay slope of 1.3. In addition to the swift observations we also present and discuss the results from a 61 ks ToO observation by XMM. (Abriviated)