Nobody was hurt in the incident, however the local cricket association, who seldom get international hosting duties have put pressure on the police to produce answers quickly.
The incident has seen security around the team beefed up as they prepare for the final match of the tour - a T20I in Hyderabad.
"The police have already arrested two persons and are investigating into the matter," Assam Cricket Association secretary Pradip Buragohain told Press Trust of India website.
"We made every attempt to ensure a foolproof security but don't know how this happened. It was near the team hotel and not at the crowded street near the stadium.
"I can assure that such incident won't occur in future again. There will be a thick security cover when the Australian team leaves for Hyderabad."
The Barsapara Cricket Stadium had attracted a sell out crowd for its first ever international match but the incident has soured the occasion.
Australia leg-spinner Adam Zampa said the incident was terrifying and a disappointing end to a great evening.
"I had my headphones on quite loud and was looking towards the other side of the bus," said Zampa.
"I just heard this loud bang. It was a pretty scary five seconds or so.
"Our security guard mentioned quite quickly that it might have been a rock. It was a pretty scary incident. You never want those things to happen. It was disappointing.
"I think everyone was alright. I think after what happened in Bangladesh with the rock as well, no one was too rattled. It was dealt with quite well, I think.
"The Indian fans are so great to us, which is one of the reasons why it's so hard to travel here. They're so loud, they love cricket and they're so passionate about it.
"Guwahati doesn't get much cricket as it is so for one person to do that and to spoil it for the rest of the Indian fans, it's pretty disappointing."