Villa, who is leaving Europe to play Major League Soccer with New York City — via a loan spell at sister club Melbourne City — was visibly upset when he was replaced by Juan Mata 10 minutes after half-time.
The 32-year-old had announced before the tournament he was quitting international football, but that came as news to Del Bosque, who must now consider his own future after a disastrous World Cup saw his side eliminated after just two matches.
“He (Villa) certainly seemed very annoyed. He said it was his last game, but I didn’t know that. I’m sure he was upset,” the Spain boss told his post-match press conference.
“All I was thinking about is that it was time to kill off the game and we did that.”
On his own future he added: “I’ll decide in the next few days or next week. There’s no rush.”
Villa scored his 59th and final international goal with a last touch of class. Andres Iniesta, winning his 100th cap, delivered inside left-back Jason Davidson to allow the overlapping Juanfran to cross for Villa to backheel past Maty Ryan.
In the second half, Iniesta’s through-ball split Australia’s centre-halves and Chelsea striker Torres — who began Spain’s gold rush with the winner in the Euro 2008 final — slid home the second, before Mata’s close-range finish with eight minutes left.
A raft of retirements are expected but Del Bosque said it was not necessary to start again from scratch.
“There’s still players who can help the national team a great deal and we must remain aware of that.
“We have to move on to another (European Championship) qualification phase next and whoever the next manager is, the future is safe.
AUSTRALIA: Ryan, McGowan, Spiranovic, Wilkinson, Davidson, McKay, Jedinak, Bozanic (Bresciano 72), Leckie, Taggart (Halloran 46), Oar (Troisi 61).
SPAIN: Reina, Juanfran, Albiol, Sergio Ramos, Jordi Alba, Alonso (Silva 83), Koke, Cazorla (Fabregas 68), Iniesta, Villa (Mata 57), Torres.
Referee: Nawaf Shukralla (Bahrain).