Sainz made contact with Alonso's Aston Martin at the second restart with two racing laps to go, which spun his fellow Spaniard around.
The race was red-flagged for a third time and the FIA opted to run the final lap to the flag behind the safety car using the previous grid order, which meant that Alonso regained his third place.
Sainz, who had recovered from losing out by pitting under the safety car brought out for Alex Albon's Turn 6 crash which then turned into a red flag that handed his rivals a free tyre change, took the final restart in fourth place.
However, he was awarded a five-second penalty for causing a collision.
Sainz was sitting in his car awaiting the resumption when told of the penalty, and he made it clear on team radio that he felt he should have been able to state his case to the stewards.
Meanwhile, rival teams were able to tell their drivers to keep up in the safety car queue in order to take advantage. In the final classification, Sainz dropped out of the points in 12th place.
With team-mate Charles Leclerc out on the first lap – co-incidentally after contact with the other Aston Martin of Lance Stroll – Ferrari failed to score in Melbourne.
"Frustration is the right word," Vasseur told Autosport when asked about the team's tough weekend.
"And today, it's even more true. There was contact between Lance and Charles on lap one, the first start, and we lost one car.
"And the situation with Carlos is very tough for the team. And the test is tough, because if you consider the race, he had to do an extra pit stop with the safety car at the beginning, and he went through the field.
"And then we can speak about the incident, if it's a race incident or not. For me, it is the same lap one story. But the frustration is probably more the fact that they took the decision in five minutes."
Asked if it would have been fairer if the stewards had talked to Sainz, he said: "And to have a look on the data. You can look at the data and know if Carlos was in a panic mode, if he already hit the brakes.
"Fernando said the penalty was a bit harsh. I think in this situation when it won't impact the [Alonso] result it makes sense."
Vasseur said he understood why Sainz had an emotional reaction to the news of the penalty.
"You have to understand the situation too that he had to do an extra pitstop at the beginning with the first red flag, that we were nowhere then, and then he had a mega comeback," he explained.
"His pace was very strong and very consistent, and he came back not far away from the podium.
"Then to lose it like this, not from nowhere but before the end, I can perfectly understand the emotion and the fact that he was in shock with that."
Vasseur said he had no concerns about the way that the FIA handled the red flag situations during the race.
"I'm not complaining because it's always difficult to take decisions when you have to do it live," he added.
"But coming back to the decision about Carlos, they had time to take the decision. In this case, they have to take time.
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"And for sure if you have to push on the button of the red flag it's another story, it's about safety, you have to do it in the rush."
