The top two met in Paisley and it was St. Mirren who were on course to stretch their unbeaten start to the season at half-time.
The Buddies led through Nikolas Agrafiotis's fiercely struck penalty after Liam Scales was penalised for handball.
But Scales made amends to start the Celtic second-half fightback when he headed home from a corner.
Yang Hyun-jun then struck the winner on the counter-attack after being fed by Camilo Duran.
Victory opens up a five-point lead for Martin O'Neill's men at the top of the table, although Hearts can close that gap to three when they face Dundee on Sunday.
Rangers continued their upturn after a difficult start for new manager Derek McInnes, but victory came at a cost with Shankland facing a lengthy spell on the sidelines.
The Scotland striker pulled up after just five minutes at Ibrox with McInnes, who coached Shankland at Hearts last season, expecting a similar layoff to the two-month spell he missed earlier in the year.
"He has a similar feeling to the hamstring injury he had at Hearts last January. We don't want to speculate too much but he says it feels similar," said McInnes.
"It's a shame for the boy because he was obviously in good form, getting himself moving and enjoying some of that attacking threat we've had over the last few games and we've waited long and hard for that."
Shankland had scored Rangers' previous three goals to secure their first league wins under McInnes but his replacement, Ryan Naderi, quickly got the goal that turned out to be the winner.
Motherwell goalkeeper Alex Paulsen gifted the German striker an open goal after trying to dribble past Naderi.
In the absence of Shankland, Kim Min-su missed the chance to open his Rangers account when he fired a first-half penalty wide.
New striker Kevin Kelsy also hit the bar as Rangers wasted a number of chances to put the game to bed but held out for a crucial three points.