Barcelona won the Nou Camp friendly 3-1 on penalties after the game finished 1-1, with Villa's close-range effort cancelled out by a stunning strike from Filippo Inzaghi.
Milan chief executive Adriano Galliani met Barca president Sandro Rosell and Ibrahimovic's agent earlier in the day and they will reconvene on Thursday for further talks.
"Negotiations will continue tomorrow," Spanish media quoted Galliani as telling the club's television station. "I have an appointment with Barca's president at midday.
"It is very complex, very difficult and very costly... At present, Barca are willing to sell (or loan) the player, he is willing to come to Milan but we are talking about a mountain of money in the middle of a crisis."
Villa, signed from Valencia before his heroics in Spain's World Cup triumph in South Africa, started up front alongside the Swede, despite the doubts about his future. Ibrahimovic had a spectacular goal ruled out for offside in the first half and was substituted at the interval.
"I don't know what the problem is," Ibrahimovic told Italian television after the game.
"The directors have told me they don't want to sell me but I don't know what the coach thinks because he doesn't speak to me. We've only spoken twice in the last six months.
"I'm happy here and I'm not a problem."
Villa flicked in the opener at the near post after good work down the left from his fellow new arrival Adriano Correia.
Inzaghi levelled with a flying volley from distance in the 67th minute, and soon after former Barca favourite Ronaldinho was substituted to a standing ovation from a packed Nou Camp.
Reserve goalkeeper Jose Manuel Pinto was the Barcelona hero at the end, saving three penalties in the shootout.
The Spanish champions start their title defence away to Racing Santander on Sunday.
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