But he has agreed to keep quiet on his sacking so the shows can go ahead, meaning fans who have already booked tickets, thought to number almost 100,000, will not be disappointed.
However the shows have been rebranded from Top Gear Live to Clarkson, Hammond and May Live.
They will not feature any Top Gear branding, show any footage from the programmes or feature The Stig.
A source said: "Jeremy, James and Richard agreed to the terms put to them to let the shows go ahead in a good spirit. They were desperate not to let the fans down.
"Part of the deal was that neither the BBC nor the Top Gear brand would be brought into disrepute.
"Effectively this meant gagging Jeremy from mentioning what had gone on. But he agreed to comply."
Clarkson, 54, is said to be "champing at the bit" to get back on stage, with the next show taking place in Belfast in May.
The tour will also see him travel to South Africa, Australia and Norway - where shows were cancelled while the BBC was deciding whether or not to sack the presenter.
It will come to a close on November 29 at the O2 in London, with the futures of co-stars Richard Hammond and James May unclear.
The pair's faces, along with Clarkson's, have both been removed from the top of Top Gear website.
Meanwhile the two final episodes of Top Gear - which were canned after the hotel bust-up - could be made from footage shot before the controversial presenter left, but insiders say they can never be screened.
The programmes are thought to show the presenters racing limousines and driving classic convertibles, but are not likely to ever see the light of day.
- AP with additional reporting by The Daily Mail