Stewart, 42, won the Sprint Cup in 2002, '05 and '11, had dropped to 18th after missing two weeks of racing since the Aug. 5 accident. He was 11th before the incident.
Stewart-Haas Racing announced Mark Martin will drive the No. 14 Chevrolet for the rest of the season. There are nine races remaining on the 2013 NASCAR schedule.
"After consulting with Tony's doctors and speaking with Tony, we agreed it was best for him to focus on his recovery," SHR competition director Greg Zipadelli said in a statement.
Martin is expected to be in the car Saturday for the Sylvania 300 in Loudon, N.H. He has been granted an early release from Michael Waltrip Racing to make the switch.
Stewart has won 48 Sprint Cup races in his career, which is 13th most all-time. He had one win this season -- June 3 in Dover, Del. -- giving him at least one race victory each of the last 15 years.
Stewart was leading the Aug. 5 30-lap Front Row Challenge at the Southern Iowa Speedway in Oskaloosa, Iowa, when, with five laps to go, a car driven by Josh Higday spun on Turn 4. The three race leaders -- Stewart, Tasker Phillips and Tony Shilling -- were involved in the subsequent crash.