The Cubs selected Rondon, who was the Indians' Minor League Pitcher of the Year in 2009, with the second pick overall in the Rule 5 Draft on Thursday at the Winter Meetings.
Rondon, 24, has been limited the last three seasons following right elbow UCL reconstruction surgery on Aug. 25, 2010. He fractured the same joint during winter ball in Venezuela in 2011.
The Cubs have been following him in Venezuela this winter, where he's pitching for Leones del Caracas and had a 2-1 record and 3.71 ERA in 19 games, all in relief. He has struck out 11 and walked five over 17 innings. Hitters were batting .172 against him this winter.
"Coming up through the Cleveland organization, he was one of the top prospects," said Cubs player development director Jason McLeod. "He's always been a prolific strike thrower with great stuff. Now he's missed the better part of three years with the elbow, and there's obviously risk involved."
Cubs coach Franklin Font is on the Leones staff in Venezuela and has filed reports on Rondon, plus the Cubs have sent their scouts to watch the right-hander. All the reports have been good, McLeod said.
"You take the risk with the elbow," McLeod said, "but if he comes in healthy, he's got a chance to not only make the team, but help the team. The way he's been throwing, his stuff is really good."
Rondon led the Indians' organization in strikeouts in 2009 with 137 and was fourth in innings pitched. He's made just 13 appearances in the last three years as he rehabs his elbow.
"He was a really good prospect with the Indians," Cubs general manager Jed Hoyer said. "We've been watching him in Venezuela this winter, and he's been throwing really, really well. He's got a great arm, and we feel we can capitalize on that he's healthy now and throwing the ball well."
Ross Atkins, Indians vice president of player development, said he wasn't surprised Rondon was selected.
"Hector is a very good pitcher that we obviously have a lot of respect for and a history with," Atkins said. "We hate to see him go, but we're happy for him in this opportunity and certainly, selfishly, hope we get him back."
Atkins' reports on Rondon's progress in Venezuela were that he was aggressive with his fastball.
"His strikeouts were a little bit down probably for Hector, but he was very aggressive and obviously very effective while he was there, and he's been healthy and durable," Atkins said. "With Hector, you're looking at a guy who was in the Futures Game and was obviously a top-tier prospect. He had a real tough break with his surgery and the procedures. The reports were good. I think most importantly for Hector, he was healthy."
Last year, the Cubs selected Lendy Castillo in the Rule 5 Draft. The right-hander, a converted infielder who had only been pitching for two seasons, posted a 7.88 ERA in 13 games and was sidelined with a groin injury. He will open the 2013 season in the Cubs' Minor League system.
The Cubs also lost four players in the Rule 5 Draft, including right-handed pitcher Starling Peralta, who was taken by the D-backs 14th overall in the Major League portion. Peralta was 5-8 with a 3.44 ERA for Class A Peoria. Among his starts was a strong outing Aug. 7 against Clinton, when he struck out 14 over seven innings, giving up one run on two hits.
In the Triple-A phase of the Draft, the Astros selected outfielder Michael Burgess with the first pick, the Cardinals took infielder Matt Cerda and the Blue Jays selected right-handed pitcher Alvido Jimenez.
Burgess was a first-round pick by the Nationals in 2007, and the Cubs acquired him in January 2011 in the Tom Gorzelanny deal. Last season, he batted .259 with 10 home runs, one triple and 22 doubles at Double-A Tennessee.
Cerda played for Class A Daytona and Double-A Tennessee last season and batted a combined .241 in 111 games with three home runs, two triples, 13 doubles and seven stolen bases. He was the Cubs' fourth-round pick in 2008.
Jimenez was 3-4 with a 2.64 ERA in 15 games with the Cubs' Mesa Rookie League team last season.
One player who was eligible for the Rule 5 Draft but not taken was Nick Struck, who was named the Cubs' Minor League Pitcher of the Year.
"With every team, you point at who you think will get taken, and then those guys don't get taken and you're happy," McLeod said. "You're happy for those kids [who are picked] to get a fresh opportunity with another organization."
A team that selects a player in the Rule 5 Draft pays $50,000 to the team from which he was selected. The receiving team must then keep the player on the Major League 25-man roster for the entirety of the next season, and the selected player must remain active (not on the disabled list) for a minimum of 90 days. If the player does not remain on the Major League roster, he is offered back to the team from which he was selected for $25,000. If his original team declines, the receiving team may waive the player.
Once a player is selected, he is automatically assigned to his new organization's 40-man roster.
With the moves, the Cubs' 40-man roster is now at 38.
Carrie Muskat is a reporter for MLB.com. She writes a blog, Muskat Ramblings, and you can follow her on Twitter @CarrieMuskat. This story was not subject to the approval of Major League Baseball or its clubs.