Two-time gold medallists Argentina thought they had salvaged a 2-2 draw in the Group B match in Saint-Etienne when Cristian Medina scored in the 16th minute of added time.
But crowd trouble ensued and the players were taken off the pitch before Swedish referee Glenn Nyberg had blown for full time.
For some time the outcome of the match was completely unclear, with the official IOC website indicating it had ended.
But the sides finally reappeared two hours later to play out three more minutes in a stadium by now emptied of spectators.
Medina's goal was also eventually disallowed for offside following a VAR review, and Morocco -- for whom Soufiane Rahimi scored twice -- held on to claim all three points.
"I have not been a coach for long, but never in my career as a player have I seen a situation like that," said Mascherano, who was in the Argentina teams that won the gold medal in 2004 and 2008.
"It is a circus. But that is how it is. We cannot control it. I told the boys that now we need to look forward, try to get the six points that will allow us to qualify and that all this should fill us with energy and anger for what we have ahead of us."
Mascherano said the captains of the two teams had agreed not to restart the game after Medina put the ball in the net, as projectiles including plastic cups and bottles rained down and spectators invaded the Stade Geoffroy-Guichard pitch.
"The captains decided not to play on at that point, and as time went on different versions (of events) started to appear," he said.
"The annoying thing is that the match was suspended. If you are going to review something, review it just after the incident," he said of Medina's disallowed goal, which appeared to be the equaliser after Giuliano Simeone had earlier pulled one back.
"At no point were we told the goal was not valid."
Of the decision to bring the players back out later on to complete the match, he added: "They called FIFA. I don't know who took it, but everyone was involved.
"It is a disgrace that this should happen and poison the tournament. This wouldn't even happen in a neighbourhood tournament. It's pathetic.
"Beyond the Olympic spirit, the organisation needs to be up to standard and at the moment, unfortunately, it is not."
Argentina are due to play their second match on Saturday in Lyon against Iraq, with Morocco playing Ukraine in Saint-Etienne the same day.
