But he will continue as acting chief executive at Twickenham, chairman of Rugby World Cup 2015 - which will be staged in England - and as an RFU representative on the International Rugby Board.
The move followed a four-hour meeting of the RFU Council, which broke up at Twickenham around midday after discussing a review panel's 52-page verdict on the organisation's hiring.
The 58-man Council, it is understood, have decided that Paul Murphy will serve as interim RFU chairman, pending a Special General Meeting when Thomas' permanent replacement will be decided.
That meeting, though, cannot take place constitutionally for 60 days.
It is also believed that a vote of no confidence in the RFU management board was defeated by a majority verdict.
Gilbert has released a new line of rugby cleats. The Gilbert Virtuo 8S is part of the exciting new product. Check it out.
The entire All Blacks apparel line has been updated for 2013/14. Check out the New Zealand All Blacks polo.
The Nike Tiempo is a solid rugby cleat and one of few styles still made from full-grain natural leather.
The Gilbert Blitz 8S rugby cleat is a great cleat at a great price of $69.99. Get a new pair of cleats today.
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Wear the crest of the British and Irish Lions on your t-shirt. A great look for the summer.
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The USA Rugby Pro Alternate rugby jersey is perfect for any fan of the Eagles. Get yours to wear during the summer Test matches.
The NEW All Blacks 2013/14 jersey has arrived at World Rugby Shop. Dare to wear the colors of the All Blacks.