The Northern Ireland international agreed the deal, which includes the option of a third year, following negotiations with the Scottish Premiership club in recent weeks.
Manus has played a key part in helping St Johnstone become an established top-six club, and was a major factor in delivering the Scottish Cup to Perth for the first time in their history last season.
Saints boss Tommy Wright said: “I am absolutely delighted that he has signed as he has been one of the top goalkeepers in the country over the last three seasons and I am happy that his long-term future is now secure. He’s committed for two years with an option beyond that, so we are all pleased.
“We’ve been speaking for some time now but there was never any problem – Alan has always just liked to take his time when considering his future which he is absolutely right to do.”
The 32-year-old, who joined St Johnstone in the summer of 2011, confirmed he is happy to extend his stay in Perth.
Mannus said: “I’m delighted to sign for two further years. I’ve thoroughly enjoyed my time here so far and I could not have hoped to have been treated any better by everyone within the club and the supporters.
“I look forward to finishing the season part of a squad who hopefully secure a place in the top six and then hopefully contribute to another good season next year and beyond.”