The Red Sox lost the bidding war over Twins pitcher Johan Santana, but they kept the ace from staying in the A.L.

AP / Duane Burleson

Believe it or not, the Red Sox won the negotiations for pitcher Johan Santana — sort of.

Even though the two-time Cy Young Award winner is heading to the New York Mets in exchange for four prospects, Boston kept the highly talented left-hander out of the American League and away from that other New York team — the Yankees.

In exchange for Santana, the Minnesota Twins are getting outfielder Carlos Gomez and pitchers Phil Humber, Deolis Guerra and Kevin Mulvey. The deal is still pending because the Mets must negotiate a new contract with Santana. They have between 48 and 72 hours to get the pact done and he also must pass a physical.

Sure, the Red Sox would love to have added Santana to an already potent starting rotation along with Josh Beckett, Curt Schilling and Daisuke Matsuzaka because it would have been devastating for opponents. But Boston will be able to keep its core of young talent in place for the upcoming season and the future.

The names reportedly on the table as an asking price for Santana’s services were Coco Crisp, Jon Lester, Jacoby Ellsbury, Jed Lowrie and Justin Masterson. Phone calls made to Lester and Ellsbury were not returned, but Lowrie said he’s quite happy he’s staying in the Boston organization and that all the rumors have finally ended.

“I can’t say I put serious thought into [the possibility of being traded],” said Lowrie. “But as soon as I heard my name being tossed around I thought about playing for the Twins. That’s not a bad thing and I’m not saying I didn’t want to be with the Red Sox, I’m just saying that was a distinct possibility and it was something I had to keep in mind. I’m glad to be with the Sox and obviously it’s a first-class organization.”

Santana talks fueled the winter meetings in Nashville last month, but from the time Red Sox management returned to Boston without a deal until most recently, things hadn’t changed much. The pitcher reportedly set a deadline and the Twins met it yesterday.

Here’s how things broke down and possibly the reason why the Twins decided to deal with the Mets instead of the Red Sox.

Crisp and Lester will both be arbitration eligible in the next couple of years, while the four players — Gomez, Humber, Guerra and Mulvey — have less than a half-year of major-league service, so the Twins won’t have to deal with their arbitration cases and contracts until much further down the road.

Since the Twins recently resigned first baseman Justin Morneau and outfielder Michael Cuddyer to long-term deals, there was probably no chance to re-sign Santana, especially since he turned down a four-year, $80-million extension offer. Morneau inked a six-year deal worth $80 million, which is the largest in club history, while Cuddyer signed for three years and $24 million.

The Twins also brought in Delmon Young via trade from Tampa last November. The highly talented 22-year-old outfielder will replace Torii Hunter, now with the Angels after signing as a free agent during the offseason.

It’s not like the Red Sox just sat back and waited for Minnesota to make a decision, Boston’s baseball ops personnel held meetings the last couple of days in order to come up with a package that would entice the Twins.

The Mets’ package was simply more attractive.

Here’s something else that the Red Sox possibly would have had to deal with. In order for Santana to waive his no-trade clause with the Twins, he is expecting a history-making salary for a pitcher in the range of $150 million for six years. Yes, he is one of the premiere hurlers in the majors, but if the Red Sox were to give him that kind of contract how do you think Beckett would have felt, making twice as less per season? When asked about it during the offseason, Beckett told the Boston Herald’s Rob Bradford he wasn’t concerned with that scenario.

Even though Santana would have fit nicely into the Sox rotation, the southpaw hasn’t enjoyed much success at Fenway Park. He has a career 1-3 record with a 6.89 ERA and 12 strikeouts in 15 2/3 innings of work at the storied ballpark. He did not pitch in Boston last season.

Now what?

The Red Sox have no need to worry because the club is set up for a back-to-back championship run as long as everyone stays healthy in 2008. In fact, manager Terry Francona recently said he is quite happy with the Sox’ roster, and if no changes were made it would make spring training a lot easier.

Crisp and Ellsbury will battle for the starting position in center field and, if the Sox’ pitching staff remains intact through spring training, the Red Sox will have some interesting decisions to make with Tim Wakefield, Lester and Clay Buchholz all vying for a spot in the rotation.

So, Santana is off to the National League and won’t be a help or hindrance for the Red Sox.

jmcdonal@projo.com