Rooney's brace came either side of a Grant Munro header as the Premier League side comfortably saw off their lower-league opposition.
A Roy McBain snapshot after two minutes was a rare effort on goal by Caley Thistle in the opening stages as Peterhead set about nullifying the attacking threat of the hosts.
Conor Gethins even had a half chance to give the Blue Toon a surprise lead as he connected with a cross ball on the half volley, but his effort flew high over Jonny Tuffey's crossbar.
Inverness continued to probe, however, and they were gifted the opening goal of the game after 32 minutes.
Russell Duncan's pass through to Jonny Hayes took the winger away from goal, but he was clipped from behind by Peterhead goalkeeper Paul Jarvie who had strayed well off his line.
Referee David Somers immediately pointed to the spot and Rooney, fresh from his brace in Caley Thistle's 4-0 triumph over Dundee United at Tannadice three days ago, powered the spot-kick into the bottom corner.
Hayes was also involved in the home side's second goal six minutes later.
The Irishman managed to dig out a cross from the left hand side and with the Peterhead defence on the back foot, Munro firmly planted a close range header past the despairing Jarvie.
Caley Thistle continued to threaten and Jarvie had to use all of his frame to keep out Rooney's header from a Hayes free-kick, but he was left with no chance in the 49th minute as Inverness extended their lead.
A wonderful turn by Eric Odhiambo saw him feed a through pass to Rooney and he produced a deft touch to poke it between Callum MacDonald's legs before dispatching with aplomb from 12 yards for his fourth goal of the season.
Munro then went close to scoring again moments later, but Jarvie did enough to take the sting out of the shot before Daniel Moore cleared it off the line.
Inverness were now dominating the match and Duncan came close to emulating his goal in the rout of Dundee United only for his 25-yard effort to strike the upright and bounce to safety.
Odhiambo and substitute Graeme Shinnie both had opportunities to put further gloss on the final scoreline, but it was all academic as Caley Thistle cruised to victory.