The Ireland fly-half went off four minutes into the second half with what appeared to be a right knee problem.
But with Jordan Larmour in sparkling form Leinster absorbed the loss of Sexton to run out comfortable winners.
Northampton's first meaningful test in pursuit of a quarter-final spot ended in a seven-try defeat that places them under pressure for the return fixture in Dublin next weekend.
The Premiership leaders had been superb until colliding with Leinster, catching the eye with an attacking style that was matched by results in the form of six wins from seven outings.
But they were taught a lesson in European rugby by the four-time champions who fielded greater firepower in most departments and who were able to call on a watertight defence to contain Northampton's assault in the final half-hour.
A seventh win in eight meetings between the rivals places Leinster in full control of Pool One.
It took only 131 seconds for Leinster to draw first blood as they pounced on a Northampton mistake in midfield with full-back Larmour tearing downfield before sending James Lowe over.
Clean line-out ball enabled Saints to respond as Ahsee Tuala and Teimana Harrison made big carries through the middle and, when the move swept left, quick hands ended with Tuala diving over in the right corner.
Larmour's scorching start continued as he took Sexton's clever inside ball and stepped his way into space, offering scrum-half Jamison Gibson-Park sight of the line only for Cobus Reinach to capitalise on a moment's hesitation with a covering tackle.
Leinster were not to be denied however and, after several surges, Rhys Ruddock forced his way over.
Dan Biggar's accuracy from the kicking tee, combined with his cunning break-up field, helped Northampton regain the lead against the run of play – but they were unable to score again.
After a bright spell from Saints, when they profited from being more direct, Leinster built pressure once more and their power from close range was irresistible as prop Andrew Porter burrowed a path through the home pack.
The second-half opened with another searing run from Larmour and his injection of pace was the prelude to waves of forward carries that ended when Cian Healy touched down.
It was the worst possible start to the second-half for Saints and they were in danger of being blown away as the European heavyweights immediately renewed their attack through Garry Ringrose and Robbie Henshaw.
This time Ross Byrne was on hand to finish and to compound home misery co-captain Alex Waller was sent to the sin-bin for a shove from behind moments before the try was scored.
Sexton's exit failed to affect Irish momentum but a setback did arrive in the form of a yellow card for Ringrose for his tip-tackle on Biggar, who had recovered from a toe injury to take his place at fly-half.
Leinster's defence held firm as Northampton cranked up the intensity but a series of handling errors at key moments proved costly, while even giant wing Taqele Naiyaravoro was unable to make any impression.