Thompson alleged a small group from the Free Syrian Army deliberately guided the vehicle in which he and his Channel 4 News colleagues were travelling into what he described as a "free-fire zone" on a blocked road in "no man's land" in the vicinity of the city of al-Qusayr, because "dead journos are bad for Damascus".
He also claimed UN vehicles the Channel 4 News team were travelling with later abandoned them when they were surrounded by "shouting militia".
Thomson said after being led into no man's land between Syrian army and rebel forces by four men in a black car, his team were fired upon and forced to take evasive action, eventually managing to "floor it back to the road we'd been led in on". The incident took place last weekend and Thomson is now back in the UK.
"Suddenly four men in a black car beckon us to follow. We move out behind," Thomson wrote in a Channel 4 News website blog published on Friday morning.
"We are led another route. Led in fact, straight into a free-fire zone. Told by the Free Syrian Army to follow a road that was blocked off in the middle of no-man's land," he added.
"At that point there was the crack of a bullet and one of the slower three-point turns I've experienced. We screamed off into the nearest side-street for cover. Another dead-end.
"There was no option but to drive back out on to the sniping ground and floor it back to the road we'd been led in on. Predictably the black car was there which had led us to the trap. They roared off as soon as we re-appeared.
"I'm quite clear the rebels deliberately set us up to be shot by the Syrian army. Dead journos are bad for Damascus."
Thompson said this conviction was only strengthened half an hour later when "our four friends in the same beaten-up black car suddenly pulled out of a side-street, blocking us from the UN vehicles ahead".
"The UN duly drove back past us, witnessed us surrounded by shouting militia, and left town. Eventually we got out too and on the right route, back to Damascus," he added.
"In a war where they slit the throats of toddlers back to the spine, what's the big deal in sending a van full of journalists into the killing zone? It was nothing personal."
A spokeswoman for ITN-produced Channel 4 News said: "The safety of our journalists is of paramount importance and we only ever send experienced teams into these hostile environments.
"Alex is an incredibly experienced journalist who has covered conflicts around the world for more than two decades and has used social media to share the full detail of these assignments. We will be reviewing this trip, as we do with every other foreign send and sharing the review across ITN as we continue to cover this complex and important story."