Malik had taken the first set comfortably but was down by a break of serve early in the second when he called for the trainer before taking an injury time out.
He came back on court and tried to continue but conceded the match at 1-0 in the decider.
In other quarterfinal, Ranjeet Virali-Murugesan defeated compatriot Ashwin Vijayragavan in a hard-fought three-set match.
However, India's N Vijay Sundar Prashanth crashed out of the tournament after losing his last-eight tie against The Netherlands' Mark Vervoort.
In the Doubles semifinals, Rupesh Roy and Vivek Shokeen scored an easy win over compatriots Jeevan Nedunchezhiyan and Vijay Sundar Prashanth while the pair of Abhijeet Tiwari and Ashwin Vijayragavan barely broke a sweat against Elwin Antony and Fariz Mohammed.
Results:
Singles (quarterfinals):
Mark Vervoort (NED) Bt N Vijay Sundar Prashanth (IND) 3-6 6-0 6-0.
Ranjeet Virali-Murugesan (IND) Bt Ashwin Vijayragavan (IND) 4-6 6-3 6-4.
N Sriram Balaji (IND) Bt Vijayant Malik (IND) 1-6 7-6(6) 1-0 Retired.
Joss Espasandin (SUI) Bt Austin KAROSI (USA) 6-2 6-2.
Doubles (semifinals):
Abhijeet Tiwari/Ashwin Vijayragavan (IND) Bt Elwin Antony/Fariz Mohammed (IND) 6-0 6-2.
Rupesh Roy/Vivek Shokeen (IND) Bt Jeevan Nedunchezhiyan/N Vijay Sundar Prashanth (IND) 6-1 6-1. PTI RE SHN SHN
