Sexton was unable to carry on in Dublin as Ireland saw their hopes of a second Grand Slam in five seasons slip by just seven days after a superb win in Wales.
The 27-year-old will have a scan to assess the full extent of the damage but Ireland coach Declan Kidney is hopeful that his star playmaker hasn't played his last Test of the tournament.
"He'll get a scan but he looks to have given his hamstring a bit of a tear," said Kidney.
"There will be a couple of weeks in that. How much? I think it would be wrong of me to try and second-guess. We'll know more on Monday or the next day."
With the tournament taking a break this weekend and then again after Round 3, Sexton is only expected to miss the one international match and should be back in action for the home tie with France on March 9.
He will almost certainly be replaced in the Ireland lineup against the Scots by veteran Lions tourist Ronan O'Gara, the man who took over at the Aviva against the English.
Sexton isn't the only Irishman in danger of sitting out the Scotland game and beyond, either, with flanker Sean O'Brien (tight hamstring), lock Mike McCarthy (knee ligament strain), centre Brian O'Driscoll (twisted ankle) and lock Donnacha Ryan (back) also picking up injuries and prop Cian Healy facing a possible citing complaint for an alleged stamp on Dan Cole.
Wing Simon Zebo has already been ruled out of the three remaining internationals with a broken foot, while 2009 Lions Paul O'Connell, Stephen Ferris and Tommy Bowe still aren't fit enough to feature.