The world and European champions' victory, to which Pedro contributed a 20th-minute goal, was their 39th in 44 matches under coach Vicente del Bosque, putting him one clear of his immediate predecessor Luis Aragones to set a national record.
Del Bosque said the team's end of season tour, on which they also recorded a 4-0 victory over the United States in Boston, had been a resounding success and the squad was in great shape ahead of the next Euro 2012 qualifiers in September and October.
"The important thing was to end the season on a high note after a good year," he said in an interview with Spanish television.
Striker Villa gave the visitors the lead in the fifth minute when his curling shot from a central position 35 metres out beat goalkeeper Renny Vega low to his left.
It was Villa's 47th goal in 75 internationals, extending his lead over Raul (44) at the top of the scoring chart.
After Pedro made it 2-0 with a deflected shot from Villa's assist, Alonso's strike moments before half-time found a gaping hole in the defensive wall and Vega couldn't get down in time to save, this time to his right.
"It was a tough match because of the state of the pitch and the heat," Pedro told Spanish TV. "We are all looking forward to a rest now when we can recharge the batteries."
In the second half, Spain continued to dominate but their play, dictated by David Silva, was more direct. Silva and fellow substitute Fernando Torres missed good chances.
Venezuela, warming up for next month's Copa America in Argentina, showed plenty of industry but were outclassed by the slick Spanish, who left several first-choice players, including captain and keeper Iker Casillas, out of their starting line-up.
The home side's best chance fell to Giancarlo Maldonado in the 18th minute when he sped clear into the penalty area but his low shot was saved by the onrushing Victor Valdes.
Spain have now won all three of their meetings with the "Vinotinto" - the Venezuelans' nickname for their team who wear red-wine coloured shirts.
