Johnson, who was a modified Type-A free agent, is now in line to receive a raise on the $5.85 million he made in 2011. The Blue Jays also announced they would make a corresponding roster move on Thursday to create room on the 40-man roster.
Toronto would have received two compensatory picks in next year's First-Year Player Draft if Johnson declined and left for another organization. Instead, the club can now fill its glaring hole at second base.
"We offered on Kelly Johnson because we were fine with whatever outcome," Toronto general manager Alex Anthopoulos said prior to the deadline. "Either he comes back or we get the Draft picks. We're fine, we're happy, it's a good outcome, it's a no lose for us."
Johnson came to the Blue Jays during August in a trade with Arizona for second baseman Aaron Hill and utilityman John McDonald. Johnson proceeded to hit .270 with three homers and nine RBIs in 33 games with his new club.
The 29-year-old has produced back-to-back 20-plus home run campaigns and is one of the top middle infielders available on the open market. He is a career .260 hitter with 92 homers, 335 RBIs and a .343 on-base percentage in six seasons.
There had been a lack of reported teams interested in Johnson's services, which could have something to do with the current financial situation facing many players in Major League Baseball.
"I do think the middle class is starting to be phased out in the game, because I think a lot of teams are saying, 'We'll just go with young players,'" Anthopoulos said. "The elite players are getting paid elite dollars, but other than that I think the middle class is being phased out."
The Blue Jays are expected to make Johnson their starting second baseman in 2012. He also has the ability to play left field, but with Travis Snider and Eric Thames already in the mix at the position, there wouldn't appear to be room for anyone else.
Toronto will have six picks in the first two rounds of the 2012 First-Year Player Draft. Toronto has two first-rounders, one of whom is a compensation pick for being unable to sign its top pick -- Tyler Beede -- last year.
The Blue Jays will also have their own second-rounder and three compensation picks, one each for losing Jon Rauch, Frank Francisco and veteran catcher Jose Molina to free agency.