Bumrah's yorker during Wednesday's session at the Hampshire Bowl left Shankar with a bruised toe, and the all-rounder skipped the nets on Thursday.
Bumrah said Shankar was fine ahead of Saturday's World Cup match against Afghanistan after the "unfortunate" incident.
"We obviously don't want to injure a batsman...It was not the aim, it was unfortunate that he got hit. He's okay, he's fine. But you have to do all your preparations and practise all your deliveries."
Few quicks bowl at full tilt at the nets but Bumrah, currently the top ranked bowler in one-day internationals, sees it as an opportunity to hone his weapons before a match.
After their victory in the opener against South Africa, skipper Virat Kohli said Bumrah practises just like he would bowl in a match.
"The best preparation for me is to bowl to batsmen," said the 25-year-old, whose unusual bowling action and final-overs mastery make him a precious asset in the one-day game.
"Sometimes you plan for a particular batsman, sometimes you want to try something in the match. Before that you try that it in the nets.
"We want to execute everything in the nets so in the match it's just about repetition. I try to do all of that -- be it death bowling, be it a new ball thing... Whatever you feel you have to do in the match you try to replicate that in the nets."
India have lost opener Shikhar Dhawan to a fractured thumb while Bumrah's new ball colleagues Bhuvneshwar Kumar is out of the next two to three games with a hamstring injury.
KL Rahul will replace Dhawan at the top of the order on Saturday while quick Mohammed Shami is set to play his first match of the tournament.
Bumrah said the changes exemplified the depth and flexibility of the India squad.
"It shows a lot about our ability to adjust," he said, referring to Rahul's half-century against Pakistan in his first match after moving up from number four.
"That says a lot about the quality of the player. He can adjust according to situations and accelerate when he wants... So injury is not a headache for us."
(Reporting by Amlan Chakraborty in Southampton; editing by John Stonestreet)
