The incident happened as Australia travelled back to their hotel following day one of the second Test in Chittagong.
That prompted authorities to tighten security around the Australia team. No player was, however, hurt in the incident, a city police source informed.
"Guwahati stone-throwing incident NOT reflective of our security measures".
Talking about the incident, Australian leg spinner Adam Zampa told media, "I had my headphones on quite loud but (suddenly) just heard this loud bang".
"Really unfortunate incident after a great game aimed to tarnish Guwahati's reputation as emerging sports hub. We strongly condemn it", Sonowal said on his official Twitter account. We will foil the evil design with the support of the people of Assam. "Culprits will get exemplary punishment", the chief minister added.
Referring to the security arrangements put in place for worldwide sports events in the state, the chief minister cited an appreciation letter from Roma Khanna, the head of venue operation for the FIFA Under-17 World Cup.
India, however, made no further breakthroughs and Henriques - whose knock included four fours and four sixes - and Head wrapped up a convincing success with 27 balls remaining.
Sonowal said he has directed Assam chief secretary Vinod Kumar Pipersenia to conduct the inquiry and submit a report to him.
Indian Sports Minister Rajyavardhan Rathore, an Olympic silver medalist in shooting, said there were tight security arrangements in place for the Australian team as well as for the players taking part in the Under-17 FIFA World Cup. Both teams were given a rousing welcome. Assam CM asked the DGP to look into the matter and arrest those involved in it, the police also arrested a couple of youngsters this morning as a part of the investigation.