Alex Teixeira had put the Ukrainians in front before Bonucci's screamer of an equaliser, but Willian rattled the crossbar in stoppages.
"Considering the way the game was going, we certainly did well to get it back on track," the defender told Sky Sport Italia.
"We went on to the pitch a little too timid and allowed them to control the tempo. We cannot afford that, as nobody gives you an inch in the Champions League.
"Juve must always control the game from the first to the last minute. When we attacked them, we put Shakhtar under a lot of pressure."