Leading the side in place of regular captain Mehidy Hasan Miraz, who missed the match after suffering a concussion in the second ODI, Shanto watched Bangladesh post a competitive 274 for 5 thanks to contributions from Towhid Hridoy (83), Litton Das (58 not out) and Mosaddek Hossain (56 not out).
Australia chased down the target with three balls to spare, riding on Cooper Connolly's match-winning 149. However, Bangladesh pushed the visitors to the brink through a sensational spell from Shoriful Islam, who claimed 6 for 48.
"I'm really proud of the boys. Especially today, the way we came back strongly in the last few overs. That's what we need, that character in the field where everyone believes we can come back anytime," Shanto said after the match.
The stand-in skipper felt Bangladesh had enough runs on the board but admitted a lack of wickets in the middle overs proved costly.
"I think 275 was a brilliant score. The way Hridoy and Mosaddek batted, I was really happy to see. But if you look at our spin in the middle overs, we didn't get enough wickets, so that cost us the match today," he said.
Shanto reserved special praise for Shoriful, who returned to the XI after missing the first two matches and nearly inspired Bangladesh to a series sweep.
"He showed a lot of character after not playing the last two matches and coming back for this one. It's not easy, but I'm really happy with how he bowled and I hope he will continue this form," Shanto said.
The Bangladesh captain also highlighted the healthy competition among the pace bowlers, crediting it as a key factor behind the team's historic 2-1 series victory over Australia.
"I think that's what we need as a bowling unit. If you look at Taskin, Mustafiz, and some of the bowlers on the bench, they have worked really hard over the last few years. There is a very healthy competition in the dressing room, which is why we got the result," he added.
Despite missing out on a whitewash, Bangladesh secured their maiden ODI series win over Australia by taking the three-match contest 2-1.