The 31-year-old Davenport, twice former champion at Indian Wells, summoned her trainer when trailing Serb Jankovic 4-1 before deciding to withdraw after losing the first set 6-2.
"My back was injured before I came here but I got it better, got it better and then this morning woke up and just couldn't move," Davenport told reporters.
"It was pretty obvious to me after two games that I was pretty sore out there and it was quite hard to rotate.
"I was hopeful with all the medication I took and the treatments, but it just didn't happen," added the former world No. 1 and champion at Indian Wells in 1997 and 2000.
Jankovic, who will face compatriot Ana Ivanovic in the semifinals, was unaware of Davenport's injury before the start of the match.
"I just came out on the court with the goal I wanted to play her really aggressive and take the initiative from the first strike, and that's what I did today," the 23-year-old said.
"But I had no idea that she had some problems. I wish her to recover as fast as possible and to come back."
Ivanovic booked her place in the last four by brushing aside Russia's Vera Zvonareva 6-1, 6-4 earlier in the day.
The 20-year-old Ivanovic, bidding for her first WTA title of the year, outplayed her opponent in a baseline battle to seal victory in just over an hour.
"I started really well," Ivanovic said after reaching her third semifinal of the season. "I thought I played some of my best tennis here so I was really happy about that.
"In the second set, I had a break up and then lost a little bit of concentration. I started to get a bit emotional and tried to go for too much. I lost my rhythm a little bit.
"I was just happy that at the end of the second set, I managed to keep calm and play good," added the Serb, who hit 18 winners in the match to Zvonareva's 10.
World No. 2 Ivanovic, who lost to Russian Maria Sharapova in the Australian Open final in January, broke Zvonareva in the second and fourth games to breeze through the opening set in 24 minutes.
Service breaks were exchanged early in the second set before the pony-tailed Serb again broke in the ninth game when Zvonareva hit a forehand wide.
"It doesn't get easy from here," Ivanovic added. "It only gets tougher every match. Jelena and I have played many times before and we always have close matches."
Fourth-seeded Sharapova and fellow Russian Svetlana Kuznetsova, the second seed, will contest the other semifinal.