The 17-year-old became the first player born in the 1990's to score in the competition by tapping home from close range early on to give the Blaugrana victory in the Veltins-Arena.Schalke came out after the break looked more lively, but were unable to take advantage of Barça once again failing to convince in the second half of a game.
First Half
Before the encounter, the hosts had said that they felt their guests were vulnerable after having their morale sapped during a tough league defeat last weekend, but it was Schalke that looked tired and short of ideas early on.
Having set themselves sup for such a big game, Mirko Slomka's side came out and looked defensive and their fans soon became disgruntled with the unadventurous approach.
That discontentment then grew even louder in the 12th minute when Barça took the lead and set themselves on the way to a very useful away day victory.
Andrés Iniesta picked Thierry Henry's run down the left of the area; there he took aim only for Manuel Neuer to spill the shot and see the Frenchman send the rebound across the face of goal where Krkic prodded home from close range.
The goalscorer beat Cesc Fàbregas by one day to move into second place as the competition's youngest ever goalscorer behind Peter Ofori-Quaye, who still holds the record after his goal for Olympiacos a decade ago.
With the lead secured, Barcelona settled down and looked to ensure that their opponents could not have much of the ball as they played it across the midfield.
Heiko Westermann shot over just before the half-hour mark, while Samuel Eto'o sent a cross over that Krkic loked set to score for only for the impressive Marcelo Bordon to clip it past the post for a corner.
Moments before the break, Kevin Kuranyi made claims for a penalty as he was nudged by Gianluca Zambrotta when trying to meet a cross at the far post, but the referee was not impressed.
Second Half
At the weekend, Barça took their foot off the gas against Betis and saw a two-goal disappear and even in this encounter Frank Rijkaard's side showed a distinct lack of incisiveness after half-time.
The difference in this match though was that Schalke were unable to find a way through and test the Blaugrana's nerve as the home fans bayed for a goal.
Halil Altintop saw a shot deflect wide off Carles Puyol in the 49th minute before Víctor Valdés showed that he was vulnerable by pushing Christian Pander's shot back out in the area, where he was relieved to see an orange shirt reach it first.
Westermann then shot off target as Schalke continued to dominate the chances while Barça sat back and looked to play on the break. After one such counter, Iniesta came close with his shot on the run after a surge towards the area.
Fabian Ernst, Altintop and Pander all then had chances before substitute Soren Larsen wasted a glorious opportunity as a cross hit his head - rather than his head meeting the ball - and it bounced well off target.
After Zambrotta had sent over a cross that Neuer did well to stop Henry reaching, Vicente Sánchez went close as Schalke ended the game with their best spell of the match.
Bordon forced Valdés into a flying save as he met Rafinha's superb cross and Larsen then headed over moments before the referee blew the final whistle and gave Barça a crucial victory.
