They used the game to give minutes to four trialists.
Athlone Town succumbed to their second defeat in three days against Premier Division opposition.
First half goals from Jordan Gibson and John Mahon gave Sligo Rovers a commanding lead at the break.
The midlanders unloaded the bench after the break, Clara's Jack Reyonlds and new signing Jack Carlin were introduced as well as four trialists.
Ultimately the home side were unable to trouble the scoreboard for the second game in succession and Sligo debutante Johnny Kenny notched a third in the 55th minute.
The two sides will meet again in The Showgrounds on March 8th.