Lidge, an All-Star in 2005, signed for $3.975 million plus incentives, and Wheeler will get $930,000 plus incentives.
Lidge had a career-high 42 saves in 70 appearances for the NL champion Astros and was 4-4 with a 2.29 ERA. His 22 second-half saves tied a franchise record. For the last two seasons, Lidge has led all relievers in strikeouts -- 103 last season and 157 in 2004, a record for an NL reliever.
"Brad has been a huge part of our success the past few years," said Astros general manager Tim Purpura. "We are all real proud of the success he's had."
His impressive play continued into the early postseason when he saved three straight NL Championship Series games before a disappointing downturn.
He gave up two straight ninth-inning home runs, first to Albert Pujols against St. Louis in Game 5 of the NLCS and then to Chicago's Scott Podsednik in Game 2 of the World Series. He was also the losing pitcher in Game 4 of the World Series.
The 29-year-old had ERAs of 7.20 in the NLCS and 4.91 in the World Series.
In 234 career games since 2002, Lidge is 17-12 with a 2.71 ERA and 72 saves. In 17 career postseason games, he is 1-3 with a franchise-record six saves and a 2.52 ERA.
In 71 appearances last season, Wheeler was 2-3 with a 2.21 ERA and three saves. He had a first-half ERA of 1.64 and was tough at home, posting a 1.45 ERA in 35 outings.
The right-hander has never allowed a run in seven NLCS games.
He is 8-12 with a 4.18 ERA in 182 career appearances. He has also played for Tampa Bay and the Mets.
"He has quietly become one of the best setup guys in baseball," Purpura said. "People don't know much about Dan ... but he's a real steadying force in the bullpen. It's not an easy role to have to go in there and always be in the thick of things."
The Astros' only remaining arbitration-eligible player is All-Star third baseman Morgan Ensberg. He batted .283 with 36 home runs and 101 RBI in 2005, setting team records for home runs and RBI by a third baseman.
He should get a significant raise from last season's $450,000 salary.