Rangers had leapfrogged their Old Firm rivals to the summit 24 hours earlier but their lofty status was short-lived as Celtic eased to victory.
Anthony Stokes set the ball rolling before Hooper converted from the penalty spot and claimed his second shortly before half time.
Liam Miller pulled a goal back from the spot before Hooper passed up the chance of a hat-trick from another penalty.
Celtic made three changes from the side who lost the Co-operative Insurance Cup final to Rangers as they returned to action with the visit of Hibs.
Stokes, Glenn Loovens and James Forrest all started, with Thomas Rogne, Georgios Samaras and Kris Commons named on the bench.
Hibs made four changes after their derby draw with Hearts at the weekend, as Michael Hart, David Stephens, David Wotherspoon and Ricardo Vaz Te were all added to the team for the visit to the east end of Glasgow.
Celtic could have taken the lead after 25 seconds when Hooper exchanged a one-two with Stokes before unleashing the shot that was blocked bravely by Mark Brown.
The Hoops were ahead after four minutes when Emilio Izaguirre supplied the pass for Stokes and he sent an angled drive into the bottom corner.
Celtic doubled their lead with 20 minutes gone when Scott Brown was tripped in the box by Martin Scott and Hooper lashed high into the net from the penalty spot.
Celtic were still hungry for more goals and Forrest saw his shot from the edge of the box blocked, before Izaguirre ended a lovely run by blasting well over.
The home side continued to press and Hooper supplied the cut-back for Stokes but he mis-kicked in front of goal and the chance was lost.
Celtic had the net bulging again six minutes from the break, this time Hooper racing onto a Stokes pass before rifling home from six yards.
Celtic swapped Loovens for Rogne at half-time before Hibs replaced Derek Riordan with Akpo Sodje.
Neil Lennon's men still looked dangerous after the break and Hooper burst through on goal looking for his hat-trick but Brown did enough to put him off.
Izaguirre then exchanged a one-two with Hooper only to drag his effort across goal and narrowly wide of target.
Hibs pulled a goal back after 66 minutes when referee Euan Norris ruled Charlie Mulgrew had fouled Wotherspoon in the box.
Miller then held his nerve to convert from 12 yards.
Celtic could have ended any small hope Hibs had of a comeback when Stokes stood over a free-kick on the edge of the box but Brown saved well to tip the swerving effort past the post.
Commons and Freddie Ljungberg were thrown into the action late on.
Ljungberg had an impact when he was felled by Paul Hanlon in the area with 84 minutes gone but Hooper blew the chance of a hat-trick when he fired wide from the spot.