Stoke had much of the early pressure, Ade Akinbiyi squandering the best chance with only Neil Sullivan to beat.
Leeds substitute Julian Joachim was lively in the second half and had a good shot saved by Steve Simonsen.
But on 71 minutes Thomas swung and missed a David Healy cross and the ball ricocheted off his standing leg and past the helpless Simonsen.
Leeds manager Kevin Blackwell:
"I spoke to Mr Bates on the phone this morning but it was only a short chat.
"It was literally, `hello, how are you?' but I'm expecting us to sit down and have dinner on Wednesday or Thursday next week.
"I don't know where my future lies in the long term but hopefully it will be at Leeds during the short term."
Stoke: Simonsen, Buxton, Thomas, Taggart, Hill (Asaba 83), Russell, Brammer (Eustace 86), Jarrett, Clarke, Akinbiyi, Noel-Williams (Greenacre 55).
Subs Not Used: Hall, de Goey.
Leeds: Sullivan, Kelly, Carlisle, Butler, Pugh, Richardson, Wright, Gregan, Lennon (Joachim 45), Deane (Ricketts 69), Healy.
Subs Not Used: Harrison, Einarsson, Spring.
Booked: Pugh, Deane, Ricketts.
Goals: Thomas 72 og.
Ref: I Williamson (Berkshire).