The sides enjoyed contrasting fortunes when they qualified for next year's finals in South Africa, Spain winning all 10 matches and Argentina flirting with elimination and it was the home team that took early control at a packed and boisterous Calderon.
After paying tribute to Germany goalkeeper Robert Enke, who committed suicide on Tuesday, before kickoff Spain's midfield orchestrators Xavi and Andres Iniesta took a grip and it was no surprise when Alonso put them in front on 16 minutes.
Goalkeeper Sergio Romero could only parry David Silva's shot into the Real Madrid midfielder's path and he finished powerfully and high from close range.
Spain almost doubled their lead on the half hour but defender Fabricio Coloccini somehow blocked David Villa's fierce drive on the line with Romero stranded.
Vicente del Bosque's side had less control in the second half and Argentina looked more dangerous.
MESSI PENALTY
Lionel Messi equalised with a 61st-minute penalty after the referee ruled substitute Raul Albiol had brought down Maxi Rodriguez.
Defender Martin Demichelis then handled and Alonso rifled home the spot kick with four minutes remaining before substitutes Alvaro Negredo and Jesus Navas went close to a third for Spain.
"The first half belonged to them but the second half was all us," Argentina coach Diego Maradona told a news conference. "It was a very even match and in general I am satisfied."
Spain goalkeeper and captain Iker Casillas made his 100th international appearance.
"It's never easy to play against Argentina. We have beaten a world champion," Casillas told Spanish television.
Spain and Argentina have now met 12 times and have five wins each, with two draws.
