The Irishman, one of seven changes to Neil Lennon's side, struck his 21st goal of the season from close range in the 29th minute after strike partner Mo Bangura had caused some confusion in the visitors' defence following a Hoops corner.
Celtic stand-in goalkeeper Lukasz Zaluska made a good save from Saints midfielder Murray Davidson just before the interval and Bangura struck the post after the break but the match was generally free from excitement and the champions ran out comfortable winners.
Lennon, as promised, utilised his squad but it would have been difficult to judge his fringe players in such a low-key match.
Full-back Mark Wilson, whose last game was on October 29, came back in as captain, along with number two keeper Zaluska, defenders Kelvin Wilson and Thomas Rogne, midfielder Dylan McGeouch - making his first start - Stokes and Bangura, who was back for the first time since December.
Out went Adam Matthews, Charlie Mulgrew, Scott Brown, Georgios Samaras, Fraser Forster and Gary Hooper, the latter two starting on the bench.
Saints manager Steve Lomas also reshuffled his side following their 5-1 defeat by Motherwell at the weekend.
Defender Callum Davidson, midfielders Chris Millar and Jamie Adams and striker Cillian Sheridan came in with Frazer Wright, David Robertson, Marcus Haber and Derek Riordan dropping out, the last two named among the substitutes.
Lennon took his place in the stand after being handed an immediate three-match touchline ban today for confronting referee Euan Norris after last month's William Hill Scottish Cup semi-final defeat by Hearts.
The former Celtic skipper, who had just served a two-match touchline ban for criticising referee Willie Collum following March's Scottish Communities League Cup final defeat by Kilmarnock at Hampden, received a six-match ban in total with half of the punishment suspended until the end of next season.
Lennon had one of the best views in the stadium as he watched his makeshift side struggle, understandably, to get into any sort of rhythm in the early stages.
There was little action at all until Stokes gave the home side the lead just before the half-hour mark and it came after the Hoops were awarded what looked like a contentious corner, when Liam Craig tackled Stokes.
McGeouch's corner eventually arrived at Mark Wilson who played it in to the box and when Bangura's mis-hit shot came across Saints keeper Alan Mannus, Stokes was waiting to tap into an empty net, the visitors appealing for offside to no avail.
Moments later, as the home side warmed to their task, Bangura's long-distance shot was saved down at his left post by Mannus.
In the 36th minute, at the other end, Craig fired a free-kick from 25 yards wide of Zaluska's left post, not allowing the almost redundant keeper to see some real action.
Seconds from the break, though, Zaluska made a good point-blank save from Davidson after the Hoops defence had been opened up by Jody Morris.
Celtic took heed of their warning and within minutes of the restart Mannus was forced to parry a powerful drive from midfielder Joe Ledley with Kris Commons putting the rebound high over the bar.
The Scotland midfielder, desperately looking for a goal to follow his first of the season against Rangers at the weekend, had another effort in the 53rd minute, this time from a free-kick from 20 yards, after Saints stopper Steven Anderson had fouled Bangura, but he arrowed his drive straight at Mannus.
Bangura came close two minutes later when he struck the base of the near post with a shot, after being played in by Stokes.
There was enough hesitation at times in the Celtic defence to give St Johnstone some encouragement, Morris taking advantage of a mix-up to try a delicate chip from 25 yards which sailed past the far post.
With the match drifting, Hooper came on for McGeouch, Mark Wilson was replaced by Cha Du-ri and Rabiu Ibrahim made his debut when he came on for Commons.
Celtic were in cruise control but 10 minutes from time a great ball across the six-yard box from St Johnstone right-back Alan Maybury needed only a touch but found no takers.
In the first minute of stoppage time Hooper deprived Ibrahim of his first Celtic goal when, with the Nigerian substitute's close-range shot going in, he helped the ball over the line only to be flagged offside.
There was then more drama when linesman Raymond Whyte injured himself running up the line and had to be replaced by fourth official David Somers for the last few seconds.