The Cardinals lost shortstop prospect Allen Cordoba to the Padres in the Rule 5 draft on Thursday. (Baseball America)

By Rob Rains

When the Cardinals had to make decisions about which prospects to add to the 40-man roster this winter, they took a calculated risk that a major-league team would not select a player who was still in rookie ball, knowing that to keep him he would have to remain on their major-league roster for all of next season.

They left shortstop Allen Cordoba, who turned 21 on Tuesday, off the 40-man roster, which made him available to all teams during the Rule 5 draft of unprotected players Thursday at the winter meetings.

It took about three minutes for the San Diego Padres to select Cordoba with the third overall pick.

Cordoba played at Johnson City in 2016, where he won the Appalachian League batting title with a .362 average. This came a year after he was named the MVP of the Gulf Coast League, where he hit .342 to lead that league.

Baseball America ranked Cordoba as the 13th best prospect this season in the Appalachian League.

There was speculation before the draft that the Padres were going to trade Cordoba to the Minnesota Twins in a swap of players picked in the draft, but they instead held onto Cordoba and sent another player to Minnesota. Through that deal and another trade with the Reds the Padres ended up with the top three players selected in the draft.

Now the Padres will have to decide if they value Cordoba enough as a prospect to keep him on their 25-man roster, even though he likely won’t be used very much, mostly as a defensive replacement and a pinch-runner.

If the Padres decide not to keep Cordoba, they would have to offer him back to the Cardinals for half of the $100,000 fee they paid to select him.

Instead of protecting Cordoba, the Cardinals kept several players on their 40-man roster with more experience even though most rankings consider Cordoba, a native of Panama, a far better prospect.

Cordoba likely was the third best shortstop prospect in the Cardinals’ farm system, ranking below Delvin Perez, a first-round pick last year who did not have to be protected, and Edmundo Sosa, who was added to the 40-man roster.

It was the second consecutive year the Padres plucked a player from the Cardinals during the Rule 5 draft. They selected pitcher Luis Perdomo last year and did keep him on their roster for all of this season.

The Cardinals did not make a selection in the major-league portion of the draft, even though they have one open spot on their 40-man roster after releasing Seth Maness last week, just one of the moves which could have been done earlier in order to open up a spot for Cordoba on the roster.

In the minor-league portion of the draft, the Cardinals added one player and lost two. They picked outfielder Austin Wilson from the Mariners’ organization, and lost shortstop Matt Williams to the Angels and relief pitcher Kyle Grana, a St. Louis native, to the Dodgers.

If Wilson’s name sounds familiar, it’s because he was a 12th round pick by the Cardinals in the 2010 draft out of high school but turned down the team’s offer to go to Stanford. He probably would have been a first or second-round pick without his college commitment, and was indeed drafted in the second round by Seattle three years later following his junior year in school.

Wilson has not had as good of a start to his professional career as the Mariners had hoped, which is one of the reasons he was available in the draft. Wilson, 24, has spent the last three years in Class A, including back-to-back seasons in the California League in 2015 and 2016.

In 2014, playing for Clinton in the Midwest League, Wilson hit .291 with 12 homers and 54 RBIs, but saw his average drop to .239 in 2015 and .226 this season, although he did hit 13 home runs.

Wilson has primarily played right field during his years with the Mariners. Depending on how he plays during spring training, it is probable that Wilson will begin next season at Double A Springfield.

Follow Rob Rains on Twitter @RobRains