Marsh and Lyon were both left out of the ODI squad in order to be rested ahead of a "busy summer schedule" and both have been left out again to continue to play Sheffield Shield cricket for their states.
"We know coming off the back of the tour to the UAE, a huge summer at home, and the World Cup and Ashes just around the corner that we have to get the balance right between playing our best T20 team and preparing for the upcoming Test series," Australia coach Justin Langer said.
"While I know all four have a desire to be playing cricket for Australia in every format, with a really tough Test series against India coming up, we believe their best preparation is to go back and get some really good cricket under their belts in the Sheffield Shield."
Marsh played two T20Is in the UAE while Lyon played just one. Starc did not play any due to a hamstring niggle and Siddle stayed in the UAE as cover for Starc but also was not called upon.
Stoinis returns to the T20I fold. He played in the triangular tournament in Zimbabwe mid-year but was left out of the UAE squad while he recovered from a minor injury.
"Marcus missed our recent T20 matches in the UAE because he hadn't resumed bowling, but now he's back to full fitness he'll add great depth to the squad," Langer said. "Marcus is such a versatile player, he's a powerful middle-order batsman and he provides us with another solid bowling option."
Behrendorff played two T20Is in India in October 2017 and took 4 for 21 in Guwahati before breaking down with stress fractures in his back in November 2017. The WA and Perth Scorchers quick returned in the JLT Cup and impressed in the Prime Minister's XI match against South Africa in Canberra, taking 3 for 35.
"It was exciting to see him bowl well in the JLT Cup and in the recent Prime Minister's XI match, and it gave us more evidence of how devastating he can be with the new ball," Langer said. "Tactically we believe it's important to have a good left-arm swing bowler at our disposal for the four matches."
Behrendorff, Ben McDermott and Andrew Tye have all been included in the Cricket Australia XI team to play South Africa in a warm-up T20 in Brisbane on November 14 with the rest of the squad currently involved in the ODI series.