Bianchi (Marussia) collided with a recovery vehicle that was dealing with a similar incident involving Adrian Sutil (Sauber), which ultimately led to a rain-hit race finishing on lap 46 on Sunday.
Hamilton, having qualified in second, had already taken the lead and built a substantial lead over Mercedes team-mate Nico Rosberg by that point.
The 2008 world champion, therefore, claimed a maiden win at Suzuka - and 30th in total - although Hamilton's thoughts were unsurprisingly on Bianchi, who went to hospital unconscious.
Hamilton told Sky Sports: "It's a real anti-climax to hear that another driver has been seriously injured.
"I could not see what was going on and I really hope he's OK."
Felipe Massa suggested conditions were dangerous towards the end of the race, although Hamilton did not concur.
He added: "Conditions were not that bad. It was wet, obviously, but I have experienced much worse.
"It started to rain a little bit more but it didn't cause me too many problems."
Victory for Hamilton puts him 10 points clear of Rosberg in the drivers' standings with four races of the Formula One season left.
The Brit added: "It's been an interesting weekend.
"Obviously a great result for the team. To have the result, this has been a great weekend with the car.
"Qualifying obviously wasn't perfect for me but generally the car was absolutely fantastic through the race and once I was passed Nico I was able to really manage the gap and enjoy the ride."