Radja Nainggolan scored a late goal to send Belgium into the last 16 and Sweden packing from Euro 2016.
Belgium needed a point while Sweden required a shock victory to add their names to the list of 16 for the knockout phase.
Alex Witsel had the match’s first shot but failed to keep his second minute effort on target.
It was all Belgium in the opening 20 minutes before Zlatan Ibrahimovic had his volley blocked by Spurs defender Toby Alderweireld in the 22nd minute.
In the 25th minute Kevin De Bruyne attempted to break the deadlock but his shot was easily dealt with by Isaksson in the Swedish goals. The Manchester City playmaker was in the thick of things five minutes later but his shot was wide of target.
Thomas Meunier missed the best chance of the half on the stroke of half time after failing to get a full header on De Bruyne’s cross, allowing Sweden to head into the break on level terms.
The second half continued in the same manner as both sides traded jabs without landing a powerful blow until the match went into overdrive as Belgium pressed for a winner.
Lukaku failed to hand his side the lead after Isaksson stood tall to deny him a close range winner in the 70th minute.
Lukaku was denied a goal by the linesman shortly after that effort by the linesman. The Everton forward was marginally, but correctly, ruled to be offside before springing clear and dinking his finish over the Swedish goalkeeper.
Ibrahimovic was foiled in his bid to steal the headlines in the 75th minute as Thibaut Courtois palmed his fizzing free kick away from danger.
In the 80th minute substitute Dries Mertens tested Isaksson, who despite misjudging the strongly-hit shot, got enough behind the ball to deflect it away from danger. Like the numerous corners before, Belgium were unable to make the set piece count.
De Bruyne made a telling contribution in his own half as he cleared the ball of his own line from a free kick as Sweden through everything at Belgium in search of a winner.
The City star’s defensive work was made to count as two minutes later as Radja Nainggolan. The holding midfielder leaving the 6′ 4 goalkeeper sprawled on the floor after a well-struck shot from just outside the area.
Ibrahimovic attempted to prolong his international career but his acrobatic effort went just wide as the clock ticked away; Courtois clinging onto a clean sheet.
Belgium pushed for a second but De Bruyne pulled his shot wide before Benteke was denied a goal after firing straight at Isaksson.
Belgium now move on to Toulouse to play Hungary on Sunday night.