With only four first-class caps to his name, batting allrounder Cooper Connolly replaced third front-line off-spinner Murphy at the toss on Thursday as Australia began the hunt for a rare series win in Asia.
At stumps, Sri Lanka were 9-229 after choosing to bat.
Much was made of Connolly providing a second left-arm off-spin option next to Matt Kuhnemann, the leading wicket-taker in the triumphant first Test.
But it was mostly for his batting that Connolly was selected ahead of the specialist spinner, with his average 61.8 in first-class cricket compared to Murphy's 15.3.
Australia are now fielding recognised batters down to No.8 on a deck that is already showing cracks, and will become very tricky for the batters the longer the game plays out.
"First-innings runs are going to play a huge role in whoever wins this game," said bowling coach Dan Vettori.
"The anticipation that the wicket would probably be slightly more extreme than the first Test match, we thought that the number of overs would come down and maybe batting would come to the fore.
"It's an incredibly tough call on 'Murph' because I think whenever he's come into the team, he's done a fantastic job.
"It was just our interpretation of the wicket led us to believe that runs were going to be at a premium."
Connolly is yet to take a first-class wicket in his four matches for Western Australia and bowled only three overs on day one.
When Australia were struggling for a breakthrough in the third session, he was thrown the ball for only one over.
But Vettori said Connolly had already taken big strides with his bowling during the team's Dubai preparation camp and training sessions in Galle.
"He's in the team as a batsman and therefore it's a blank canvas for his bowling," he said.
"The amount of overs he's bowled in Dubai and now in the 10 or so days we've been in Galle, it's probably the most he's bowled in his career.
"He's going through a learning stage, understanding what it takes to compete on these sorts of wickets."
Vettori anticipated Connolly taking on a bigger role in the second innings as a left-armer who spins the ball into the off-stump of a right-handed batter.
"The game will speed up in that second innings and there'll be ample opportunities for Coop to come in, particular with a top-order dominated by right-handers," Vettori said.
Vettori said Australia had envisaged the day playing out differently, with Sri Lanka batting the day out.
Australia, dominant in the first Test, struggled at times for breakthrough wickets.
"We anticipated maybe not the amount of overs bowled in the first innings," he said.
"We probably anticipated the wicket doing a little bit more, it was incredibly dry compared to the first Test wicket so we thought that it would start to break up, which it has."
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