The Burton super-heavyweight narrowly lost the first round but was battling back in the second when referee Andrew Mustacchio stopped the action to disqualify the Frenchman for a head-butt.
Furious Aliev kicked his gum-shield into the empty stands at the Kokugikan Arena and remonstrated with Clarke before engaging in a sit-down protest on the ring-steps.
Clarke, who sustained a cut around his left eye, said: “I felt there was a couple of heads going in but whether it’s intentional or not I don’t know.
“I’m not going to stand here and say he did it on purpose because I’m sure he wouldn’t have wanted his Olympics to end in the way they have.
“I told him to calm down because I’ve been in those situations before. The last thing I want him to do is damage his reputation or be rude to the judges and officials, because they are only doing their job.”
Aliev’s protest did not seem likely to reach the dramatic extent of that of South Korean bantamweight Byun Jong-il, who sat in the centre of the ring for 67 minutes after losing a bout at the 1988 Olympics, delaying the rest of the competition for more than an hour.
Aliev finally moved after around half an hour, with officials having been quite happy for him to remain there since it was the last session. However, after spending 10 minutes out of the arena, he returned to resume his place.
Clarke’s win means Great Britain have guaranteed five medals at these Olympics, matching the totals from the 1956 and 2012 Games, with two more opportunities to increase that number still to come.
Earlier, Ben Whittaker edged into the men’s light-heavyweight final with a split decision verdict over Imam Khataev of the Russian Olympic Committee.
The 24-year-old from Wolverhampton becomes the second British boxer to book his place in the final after Pat McCormack was given a walkover in his welterweight semi-final over Ireland’s Aidan Walsh, who was forced to withdraw with an ankle injury.
Lauren Price is already guaranteed at least a bronze medal, while Karriss Artingstall will take home bronze in the women’s featherweight division. Galal Yafai and Caroline Dubois are yet to complete their last-eight bouts.
Ireland’s Kurt Walker narrowly missed out on a guaranteed medal when he lost his featherweight quarter-final to Duke Ragan of the US on a split decision.