The utilityman hit .253 with 10 homers and 33 RBIs in 95 games with the Rays in 2008, his first full season in the majors. He started 40 games at third base, 18 at first base, 14 as a designated hitter, six at second base and two at shortstop.
"We feel like he brings a lot to our club. ... We feel like he's going to fit in here for a number of years," Rays executive vice president of baseball operations Andrew Friedman said.
Aybar, who was seeking $1.05 million while the Rays were offering $900,000, will earn $975,000 in 2009 and $1.35 million in 2010. The deal includes a team option for 2011 and could be worth up to $6,275,000 over three years.
The terms for 2011 call for a $2.2 million salary or a $275,000 buyout.
Aybar's 2010 salary can increase to $2.1 million based on 2009 plate appearances. The figure for 2011 could rise to $3.2 million based on combined plate appearances for the 2009 and 2010 seasons.