During their first observational run, the two Advanced LIGO detectors attained an unprecedented sensitivity, resulting in the first direct detections of gravitational-wave signals produced by stellar-mass binary black hole systems. This paper reports on an all-sky search for gravitational waves (GWs) from merging intermediate mass black hole binaries (IMBHBs). The combined results from two independent search techniques were used in this study: the first employs a matched-filter algorithm that uses a bank of filters covering the GW signal parameter space, while the second is a generic search for GW transients (bursts). No GWs from IMBHBs were detected; therefore, we constrain the rate of several classes of IMBHB mergers. The most stringent limit is obtained for black holes of individual mass $100M_{\odot }$, with spins aligned with the binary orbital angular momentum. For such systems, the merger rate is constrained to be less than $0.93{\mathrm{Gpc}}^{-3}{\mathrm{yr}}^{-1}$ in comoving units at the 90% confidence level, an improvement of nearly 2 orders of magnitude over previous upper limits.