Staff at the agency were called together on Wednesday afternoon to be told of Thomas' exit and that Matthew Bull, currently the chairman of Lowe Bull Calvert Pace in Johannesburg, would succeed him.
Thomas' departure follows what has been a torrid year for the UK shop, which has suffered a series of devastating account losses.
The Lowe worldwide management group, which sanctioned the senior management change, is looking to Bull to restore the London agency to its former glory, and vie with the Lowe agency in New York in attracting more multinational business into the network.
Weeks of speculation about Thomas' future ended on Tuesday at a meeting lasting less than 10 minutes with Tim Lindsay, the president of Lowe & Partners Worldwide.
Thomas found himself under intense pressure last year as the agency was forced to resign the £43m Orange account when the loss of key personnel meant it could not be properly serviced.
The bad news was compounded by the loss of the Burger King business to Delaney Lund Knox Warren & Partners, which also took the lion's share of Lowe's £60m Vauxhall billings.
Lowe chiefs are understood not to blame Thomas for the losses, which they believe stemmed from problems that pre-dated his appointment.
But they have grown increasingly restless at the agency's failure to get on to pitchlists, and hope that Bull can bring some inspirational leadership.
Bull, 39 and a creative by background, has seen his star rise within the network since the agency he founded merged first with Lintas and later with Lowe.
Under his command, the agency has grown into the eighth-largest in the region, and has won gold three times at Cannes.
"Matthew has done an outstanding job in South Africa," Lindsay said. "He has made Lowe a real force there, building it into a top ten agency, forging a great relationship with Unilever and establishing it as a major creative powerhouse."
He added: "I know he will bring a great deal of joie de vivre and a strong sense of leadership to the London office."
Bull said: "There's no other opportunity in the world I would leave my own agency and my country for. It is a huge but irresistible challenge."
Lindsay will oversee management of the London agency until Bull takes charge in two months' time. Thomas was unavailable for comment.
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