The former Scunthorpe striker linked up with Anthony Stokes with six minutes gone to fire past Craig Samson from close range and then capitalised on a mistake by former Hoops midfielder Paul McGowan to grab a second six minutes later.
Neil Lennon's side looked in the mood to rack up a barrowload of goals but the Buddies responded impressively and fought their way back in to the game.
However, there were chances missed at both ends as Celtic deservedly secured their first win in four games as they made some amends for Thursday night when they were knocked out of the Europa League play-offs by Swiss side Sion.
The Hoops boss made two changes with Stokes and midfielder James Forrest replacing Joe Ledley and Georgios Samaras who dropped to the bench.
Perhaps the most surprising aspect of the Hoops line-up, though, was that Daniel Majstorovic had kept his place.
The much-maligned Swedish defender was heavily criticised for conceding an early penalty and consequently being sent off in the defeat against the Swiss side.
Celtic showed no sign of nerves as they raced into a two-goal lead after 12 minutes.
The first opportunity came in the second minute when Hooper sent Stokes through but he screwed his shot wide of the far post.
Moments later the Irishman had the ball in the net but referee Willie Collum adjudged him to have fouled Saints defender Marc McAusland beforehand.
But that just delayed Celtic's opener.
There were six minute gone when Stokes and Commons worked a one-two at the edge of the box to allow the former Scunthorpe striker the chance to drill his ball past Samson.
Three minutes later Majstorovic headed over from close range from a Charlie Mulgrew free-kick when he ought to have at least hit the target.
But indecision in the St Mirren defence eventually saw McGowan's pass intercepted by Hooper and he ran through and slipped the ball past Samson.
McGowan had the chance to make amends soon afterwards when Nigel Hasselbaink slipped him in with a fine pass but his effort from 16 yards was saved by Hoops keeper Fraser Forster.
Saints came back into the match and just before the half-hour mark Hasselbaink skinned Majstorovic wide on the left but his dangerous ball across goal found no takers.
As Saints increased the pressure Hasselbaink had a shot blocked by the legs of Celtic midfielder Ki Sung-yueng before Jim Goodwin, another former Celt, drove wide from the edge of the box.
Then St Mirren left-back Jeroen Tesselaar fired in a great cross from the left which was just missed by Hasselbaink eight yards out.
Two minutes after the break it took a fine save by Samson from Stokes' drive from the edge of the box to keep St Mirren in the game.
The former Hibernian striker had been allowed a free run to his shooting position which again highlighted the home side's defensive frailties.
Hasselbaink, though, was proving to be a menace in attack and after he was fouled by Celtic defender Kelvin Wilson 25 yards out, Forster was forced down to his left-hand post to make a good save from Tesselaar's free-kick.
In the 58th minute as Celtic broke with pace Samson denied Stokes with a fine near-post save at the expense of a corner which Saints defended with no great assurance.
At the other end Celtic defender Kelvin Wilson attempted a headed pass back which almost went in his own net and Celtic endured an anxious few moments before they survived the corner.
Forrest began to probe down the left and in the 75th minute he worked his way into the Buddies' box before firing in a shot which Samson stretched to his right to push past the post and again the home side held out from the corner.
As the match swung from end to end, Forster made a decent save from Steven Thompson's close-range header to conclude another Paisley attack before Samson blocked Ki's low drive at the other end after the St Mirren defence had been cut open again.
The St Mirren keeper made yet another good save from Forrest with two minutes remaining as the match slipped away from the home side who were left pondering their slack start to the game.