The alleged incident, coming months after Georgia and Russia fought a bitter war over the disputed territory, is likely to reignite regional tensions.
Saakashvili, addressing a press conference in the Georgian capital Tbilisi, said: "To go to this place was our improvisation on the way. I decided to show the [Polish] president how it looks.
"But frankly I did not expect Russians to open fire. I thought they clearly saw that this was an official cortege; this was high delegation. This place is frequently visited by EU monitors. Usually they don't do that.
"This was clearly intended as a provocation," he said.
But Russia denied its forces had fired on the convoy.
Sergei Lavrov, the Russian foreign minister, said: "When the president invites people to some kind of celebration in Tbilisi and then takes a car and takes him to another state, is it not a provocation? Of course it was.
"There was no kind of firing from our positions or South Ossetian positions," he said.
Jonah Hull, Al Jazeera's correspondent in Moscow, said: "The point to bear in mind here is that no one really knows what happened.
"I think we can accept that shots were fired, but according to different wire agency reports, shots were either fired at the convoy or into the air and nobody really knows who fired those shots, Russians or Ossetians."
Matthew Collin, Al Jazeera's correspondent reporting from Tbilisi, said: "The Polish president has been visiting Georgia to celebrate the fifth anniversary of the Rose Revolution which brought Saakashvili to power, and he wanted to show him the reality of the post-war situation on the ground.
"The Russians have generally pulled-out of what was Georgian controlled territory into South Ossetia.
"However, in a couple of places they maintained checkpoints and this was where this alleged incident was supposed to have taken place - called Akhalgori - a very tense area that used to be controlled by Georgia, but is now under the control of South Ossetian militias behind the Russian checkpoint.
Russian forces moved into Georgia on August 8 to repel a Georgian military attempt to retake South Ossetia, which has received extensive backing from Moscow.
Under an EU-brokered ceasefire, Russian forces later withdrew to within South Ossetia and another separatist Georgian region, Abkhazia, which Moscow has recognised as independent states.
But Tbilisi had accused Russia of not respecting the ceasefire by keeping forces in Perevi and in the disputed Akhalgori district.