The Blue Jays said Monday the agreement includes a $4 million team option for 2014. It was not clear whether there was an additional buyout of the option.
A hearing had been scheduled for Tuesday in St. Petersburg, Fla.
Janssen was 6-0 with a 2.26 ERA and two saves in 55 relief appearances last year, when he made $1,095,000. The 30-year-old is 21-19 with nine saves and a 3.81 ERA in 199 relief appearances and 22 starts over five seasons.
He had asked for $2.2 million in arbitration and had been offered $1.8 million.