Beeston signed a contract extension with the club and plans to retire at the end of the 2015 campaign, team owner Rogers Communications said in a release.
Beeston's contract expired in October, and there was uncertainty about whether or not he would be back with several media reports claiming the Blue Jays were looking for his replacement.
Jays chairman Edward Rogers said the team had been in discussions about Beeston's future since his contract ended.
"There were many rumours flying about, but it would have been inappropriate to comment on such matters publicly," Rogers said. "Make no mistake — we are elated to have Paul continue to lead the team for this season."
His successor will start when he retires, the release said.
"We will not be commenting on the succession process or timing," Rogers said.
The 69-year-old Beeston was the first Blue Jays employee in 1976 and has been with the ball club for 31 years, winning two World Series titles with the team.
"I love this ball club and the fans," said Beeston. "I wake up every day thinking about the game and bringing another championship north of the border. I'm excited for the season ahead — we've got a great group of guys who are fiercely competitive and hope to be playing ball in October."
Toronto made a splash in the off-season by adding Canadian catcher Russell Martin and third baseman Josh Donaldson to an already potent lineup. However the strength and depth of the bullpen remains the biggest question mark moving forward. The Blue Jays are without a proven closer at the moment after parting ways with Casey Janssen.
Beeston, a native of Welland, Ont., was named team president and chief operating officer in 1989 and chief executive officer in 1991. The Blue Jays won World Series titles in 1992 and 1993 but haven't been to the post-season since.
He left the team in 1997 to serve as chief operating officer in Major League Baseball's commissioner's office, holding that role until 2002.
Beeston later returned to the Blue Jays and was named team president and CEO in October 2009 after taking over the day-to-day operations of the club on an interim basis a year earlier after Paul Godfrey's departure.
General manager J.P. Ricciardi was fired near the end of the 2009 season and Beeston promoted assistant GM Alex Anthopoulos to the position. Together, they presented a long-term vision of a team that would consistently contend.
Anthopoulos went to work by trading longtime ace Roy Halladay, overhauling the scouting and player development system and shuffling the coaching staff.
However, the franchise's long run of mediocrity has continued. The Blue Jays have either struggled or finished near the .500 mark since the changes were made.
Anthopoulos made his biggest splash after the 2012 season. He acquired Jose Reyes, Mark Buehrle and Josh Johnson in a blockbuster trade with the Miami Marlins and added N.L. Cy Young Award winner R.A. Dickey in a deal with the New York Mets.
With expectations sky-high, the Blue Jays fell flat and finished the 2013 campaign with a 74-88 mark.
This past season, Toronto enjoyed a solid first half before fading after the all-star break. The Blue Jays settled for an 83-79 record and third-place finish in the American League East.