Kane Hemmings scored the only goal as Tranmere secured a 1-0 Sky Bet League Two win at Leyton Orient which was not enough to secure a play-off place.
The Merseysiders’ hopes of finishing in the top seven depended on them claiming victory on the day while requiring both Swindon and Sutton to fail to win, but both rivals did edge their matches to ensure Rovers will be playing fourth-tier football again next term.
Orient made the early running, with Aaron Drinan and Paul Smyth going close.
Only an upright denied the O’s from going in front in the 30th minute when a 25-yard free-kick from Tom James hit a post.
However, the visitors went ahead against the run of play in the 37th minute when Hemmings ran onto a cross from Josh Dacres-Cogley to send a close-range header into the net.
Despite much of the possession after the break, Orient failed to test the visitors’ defence although they were denied the opportunity of an equaliser in the 76th minute when referee Seb Stockbridge initially awarded them a penalty for handball before changing his mind after consulting with a linesmen.