The defending champion dropped the second set against the Spaniard but regained command in ruthless fashion to close out a 6-2 3-6 6-1 victory.
Rafael Nadal’s surprise third-round exit means the top seed’s task is less challenging and he continues to bolster his reputation as a strong contender on clay.
After seizing the first set with little resistance, Nishikori was forced on the back foot in the second set and surrendered a break with a forehand into the ??net.
Bautista Agut battled hard to retain his lead, saving three break points before he levelled the match with a booming serve.
But the Spaniard could not keep the Japanese player at bay for much longer and sent a forehand wide to gift a 3-1 lead.??
Nishikori quickened his progress with further breaks and will await the winner of Tommy Robredo’s quarter-final clash with Martin Klizan.