While Pittsburgh was undone last night by (yet another) strong performance by the Mets’ Mike Pelfrey (along with some fielding heroics on the part of Carlos Beltran, Argenis Reyes and Aaron Heilman), the Pirates organization can breathe a sign of relief after concluding their protracted negotiations with 3B Pedro Alvarez just minutes before the midnight deadline that would’ve rendered the Vanderbilt product a free agent. From the Pittsburgh Post-Gazette’s Dean Kovacevic :

Alvarez’s bonus, part of a minor league contract, far exceeded the $4 million the Pirates paid to pitcher Bryan Bullington, No. 1 overall in 2001. More striking, it was part of total spending on this 32-player draft class that approached $10 million, a figure made possible when owner Bob Nutting early last month authorized a significant increase. That total included $8,166,000 on players in the top 10 rounds and an additional $900,000 yesterday to lure the 20th-round pick, pitcher Quinton Miller.

That not only was a record for the Pirates, but it was roughly $2 million more than any major league team spent on the draft last season. The high last season was the New York Yankees’ $7.6 million.

And yet, a case also could be made that the Pirates did not end up being forced to give up all that they might have, as Alvarez, the No. 2 overall pick, wound up with the minor league contract the Pirates preferred and a bonus that ranked third overall: The San Francisco Giants last night signed catcher Buster Posey, the No. 5 pick, to a $6.2 million upfront bonus and minor league contract. A month ago, the Tampa Bay Rays signed shortstop Tim Beckham to a $6.15 million backloaded bonus.

How exactly this deal got done remains to be fully unfurled, but this much already is known: Alvarez’s agent, Scott Boras, followed his recent pattern of taking negotiations to the closing minutes before ultimately calling Huntington — the team’s lone voice in the talks — to accept. The Pirates, according to one person intimately familiar with those talks, never budged off their number, and Boras’ call came at 11:58 to accept.