Abel Ruiz converted the penalty to give Spain the lead after defender Abdoulaye Diaby clipped Cesar Gelabert's heels in the penalty box.
Spain created their first chance in the second minute when a cross by Ruiz from the right was deflected by the Mali defence and Sergio Gomez punched the rebound towards goal. Mali became the first side to retain the Africa U-17 Cup of Nations this year, beating Ghana in the final.
Spain's Real Madrid star defender Sergio Ramos will be watching the colts take on England in the Federation Internationale de Football Association U-17 World Cup final on Saturday here, sources close to the team management said. Ruiz (19th, 43rd minutes) struck twice for Spain before half-time while Ferran Torres (71st) got the third goal. Mali got a goal back three minutes after Torres' goal, through Lassana N'Diaye.
In what was touted to be a battle between Spain's finesse and Mali's force, the Europeans swept aside their Malian opponents with classy counter-attacking football. Abel Ruiz made no mistake in clinching the opener as he hit the middle of the net, leaving goalkeeper Youssouf Koita helpless. With Mali likely to keep Spain with their backs against the wall, Torres' deft touches, twists and turns, and directness can be pivotal.More news: Stranger Things star Finn Wolfhard fires agent after sexual abuse allegations surface
Mali's misery was further stretched as the African champions conceded the third goal in the 71st minute. Mali replied at the other end when N'Diaye hit the side netting in the ninth minute.
César Gelabert was the creator of Spain's first two goals. The goal was not given, and Spain went on to make it 3-0 to add to Mali's misery.
Spain was happy to soak Mali's pressure and in the 33rd minute nearly doubled its tally on the counter when Ruiz's side-footed finish, capping off a slick move from the left flank, missed the right-hand post by a whisker. That was the only piece of celebrations the African U-17 champions eventually managed in this match as Spain held on for the win.