Both teams had already booked their places at next year's tournament in Qatar but victory meant Japan finished top of Group A and lifted the gloom after a poor run of results.
Striker Shinji Okazaki headed home after some excellent build-up play in the 36th minute before midfielder Keisuke Honda nodded a second in injury-time for World Cup-bound Japan.
"I was never that worried about the team," Okada told reporters. "We knew there would be no excuses tonight and we got the result we deserved."
Japan, booed off the pitch after slumping to third place at last month's four-team East Asian championship in Tokyo, finished with 15 points from six games, three clear of Bahrain.
Okazaki was guilty of a shocking point-blank miss from a Shunsuke Nakamura cross moments before finding the net following a sweeping four-man move.
The influential Honda stooped to head home a second goal Japan's vastly improved performance merited after twice being denied by Bahrain goalkeeper Sayed Jaffar.
"I'd missed a few chances so it was relief to score one," said Honda. "I don't know what people would have said if I hadn't put one away. It was important to get the result and we have to keep this form going."
Okada paid tribute to the CSKA Moscow midfielder.
"Honda brings something different to the team," said the 53-year-old. "He keeps things simple and tidy and his energy gave the team a real boost."
Okada added: "Perhaps we should have taken our chances earlier and we got a bit bogged down in the second half but we stuck at it and got our reward, which is important."
Bahrain coach Milan Macala, whose side missed out on a World Cup place after playoff defeat by New Zealand last November, had no complaints.
"It's a fair result," said the Czech. "You could see Japan were better. The difference in the level showed."
