Celtic bossed the first half at St Mirren Park on Sunday but it was Buddies striker Michael Higdon who came closest to breaking the deadlock in the 52nd minute when his spectacular volley from 35 yards rebounded off the bar.
Both sides then missed decent chances in an absorbing second half before Hooper stabbed in the late winner, after Saints failed to deal with substitute Paddy McCourt's cut-back, to take the visitors back to within one point of Rangers.
Hoops fans spilled onto the track in celebration and after the final whistle they were hailed by Neil Lennon, who came onto the pitch no doubt a relieved man.
The Irishman had rung the changes, one of which was enforced.
Efrain Juarez came into midfield for the suspended Joe Ledley, while defender Thomas Rogne returned from a one-game ban to replace Jos Hooiveld.
Cha Du-Ri also came in for Georgios Samaras, who dropped out of the squad altogether.
St Mirren were without Paul McGowan due to the terms of his loan deal from Celtic and Hugh Murray was out with a fractured cheekbone.
Teenager Kenny McLean made his first start at home for the Buddies with Sean Lynch also finding a place in the starting XI.
Celtic were back at the stadium where a 4-0 defeat in March had ended the ill-fated tenure of former manager Tony Mowbray.
A minute's silence in commemoration of Remembrance Sunday was perfectly observed by both sets of fans.
The visitors, inspired by South Korean midfielder Ki Sung-yueng, looked sharp and purposeful in the opening stages and St Mirren found themselves pinned back in their own half.
However, despite their dominance of possession, Celtic were finding it hard to break down the Saints defence.
The Paisley side's confidence grew gradually but by the halfway point neither goalkeeper had made a proper save.
On the half-hour mark, from a Shaun Maloney corner, Celtic striker Anthony Stokes headed over the bar from 12 yards.
Three minutes later John Potter was booked for a hack at Maloney as the Parkhead skipper threatened to burst into the box following slack play in the Buddies' rearguard.
Maloney's free-kick from 25 yards was deflected over by the wall for another corner which the home side survived.
As the tempo dropped a little, Stokes had a tame effort from distance five minutes from the break which goalkeeper Craig Samson saved with ease, before Ki fired wide from a similar distance.
It took only a minute for Celtic for force their first corner of the second half but Wilson took a Maloney pass at the edge of the box and blasted high over.
Saints began to make inroads and in the 52nd minute an unexpected 35-yard dipping volley from Higdon beat goalkeeper Fraser Forster only to rebound off the bar.
In the 57th minute, just after Maloney had cleared the bar with a right-footed drive from the edge of the box, Stokes was replaced by Daryl Murphy.
Moments later Hooper's close-range header was saved by Samson down to his right when it looked certain that the former Scunthorpe striker would score.
Niall McGinn replaced Cha on the hour mark as Celtic tried to step up the pace and seconds later the Northern Ireland international squared the ball to Maloney, whose wayward shot from six yards did not even go behind for a corner.
At the other end, Forster brilliantly tipped a powerful drive from Wardlaw over the bar.
Murphy headed into the side netting at the back post from a McGinn cross from the right and, as the pressure intensified, the former Derry City winger forced a decent save from Samson with a powerful drive from the edge of the box.
McCourt replaced Juarez with 15 minutes remaining but it was fellow Irishman McGinn who had a drive from close-range well saved by Samson following a wonderful defence-splitting pass from Ki.
Higdon then sent another long-distance drive whistling past Forster's right-hand post.
The final minutes were tense as Celtic drove forward and in the second minute of added time Hooper grabbed a dramatic winner from three yards out to spark wild scenes of celebration.