Shinja Kagawa scored for Japan but they failed to cement their place at the World Cup finals on Tuesday after losing to Jordan, while Australia also slipped up against Oman.
Japan could have booked their place in Brazil in 2014 had they got a positive result in Jordan, but a 2-1 loss leaves the door slightly ajar for the rest in Asia qualifying Group B.
A win would have been good enough to see them safe but they went 2-0 down thanks to goals from Khalil Bani Attiah and Ahmed Hayel.
Japan pulled a goal back through Manchester United's Kagawa but it was not enough, leaving them on 13 points, six ahead of second-placed Jordan.
Meanwhile, in the same group Australia drew 2-2 with Oman.
With Japan looking on course to take top spot in Group B, the Socceroos are keen to shore up second place behind them and with it book their trip to Brazil.
That looked a tough ask when they fell 2-0 down but, thanks to a late fightback they at least got a point, although that was far from ideal.
As a result they have six points and can still be easily bypassed by any of the sides below them.
Had they not got a point, though, that situation would be all the more serious.
Today they were thankful to Tim Cahill for a trademark header and to Brett Holman for an 85th-minute equaliser.
Abdul Aziz Mubarak had put Oman ahead early on and Mile Jedinak's second-half own goal put Australia in big trouble, but they somehow found a way out of it.
In Group A, South Korea maintained their position amongst the pacesetters as they got the better of Qatar 2-1.
It was a dramatic finish at the Seoul World Cup Stadium, with Song Heung-min scoring a 96th-minute winner, having come off the bench with less than 10 minutes remaining.
Prior to that, Lee Keunho's opener had been cancelled out by Khalfan Al Khalfan.
South Korea were quickly replaced in top spot in their group, though, as Uzbekistan beat Lebanon 1-0.
Server Djeparov scored the only goal of the game with 64 minutes gone and they now head the table by a point, albeit having played a game more.
Jones was named on a three-man short-list alongside Exeter striker Jamie Cureton and Port Vale forward Tom Pope, who won the individual League Two prize at the weekend gala at The Brewery in London.
"If you keep yourself fit and you've got desire, and if you are lucky with injuries, you can play a lot longer these days," said Parkinson, who won the Outstanding Managerial Achievement award for guiding his side to the Capital One Cup final at Wembley.
"Look at Ryan Giggs and Gary is an example of that. He's an outstanding captain.
"We've only had him a year, but he's an inspiration on and off the pitch. To be in the top three is a great accolade for him."
Jones, who started out at Swansea in 1997 before spending most of his 16-year career at Rochdale, joined Bradford on a free transfer last summer and has already made 44 appearances for the Bantams this season.
