Neuer undid his good work shortly afterwards, though, when he could only parry Henry's sidefooted effort from a tight angle after the Frenchman had been played in by Iniesta's clever pass.
Henry latched on to the loose ball to find the unmarked Bojan at the far post, the young star slotting in from point-blank range to become the second youngest scorer in Champions League history.
Schalke striker Kevin Kuranyi headed straight at Barcelona keeper Victor Valdes soon after, but it was a rare threat on the visitors' goal as the home side failed to match the expectation that they could cause a possible upset.
And only an interception from home centre-back Bordon then prevented Bojan latching onto Samuel Eto'o's neat cross to double Barca's advantage as the Spanish side's level of control resulted in groans of frustration from the home crowd.
But Schalke pushed forward after the break and Altintop saw a deflected shot go just wide.
Christian Pander then unleashed a powerful shot which Valdes failed to gather before defender Carles Puyol cleared.
Barcelona invited pressure as they sat back on their lead and an encouraged Schalke almost made the Catalan club pay.
Altintop should have been ruled offside but was allowed to run through before dinking a shot over the on-rushing Valdes and a defender, only to see his effort across goal go agonisingly wide.
Larsen then headed wide as Schalke failed to make the most of their chances, before Eric Abidal escaped conceding a penalty when it seemed he pulled at Schalke's Heiko Westermann, who put a shot wide.
Schalke's Bordon also had a late header tipped over but Barca ran out winners as the German side paid for a slow start to the tie against vulnerable opponents.
• Schalke coach Mirko Slomka: "If you saw the second half we had plenty of chances so you can't say that there is no point in going to Barcelona.
"We know it will be difficult but we're going to give it a shot."
• Barcelona coach Frank Rijkaard: "I'm delighted for Bojan because he just does everything right on the field.
"Every decision he takes is the right one. You look at his age and then you see him performing like a great player for his team. He deserves special congratulation.
"He shouldn't lose his humility and should keep working, but really, it was a pleasure to watch him."
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