His decision to replace chief whip Dame Rosie Winterton with Nick Brown was met with some surprise last week.
MPs Holly Lynch and Conor McGinn have resigned, it was confirmed.
Ms Lynch tweeted it was "time to focus" on her marginal constituency while Mr McGinn said it was the "right time" to concentrate on his seat and his family.
A spokesman for Mr Corbyn thanked them for their service and said that their positions would be filled "in due course".
As his reshuffle continued, Mr Corbyn said 10 MPs who left the front bench in a mass walkout over the summer were returning. They are Jack Dromey, Pat Glass, Sharon Hodgson, Roberta Blackman-Woods, Kevin Brennan, Louise Haigh, Jenny Chapman, Matthew Pennycook, Nick Thomas-Symonds and Emma Lewell-Buck.
Mr Corbyn said: "I am pleased to announce the appointment of 21 MPs to our front bench, 14 of whom are women and four of whom are from the black and minority ethnic community.
"I welcome back the 10 who have returned, and look forward to working with the eight talented MPs joining the front bench for the first time."
But, in response to the removal of Ms Winterton, the chairman of the parliamentary party, John Cryer, wrote to Labour MPs to protest that he had not been kept informed about the reshuffle despite being engaged in talks with the leadership on putting some shadow cabinet posts up for election.
However, shadow home secretary Diane Abbott, a Corbyn ally, contradicted the claim. She told BBC Radio Four's The Westminster Hour: "He was consulted. We felt it was important to have a full shadow cabinet in place for Parliament coming back."
Whips are appointed to help ensure their party's discipline, including making sure MPs vote in line with the leadership.
St Helens North MP Mr McGinn clashed with Mr Corbyn in August, when he accused him of threatening to use Mr McGinn's father, a Sinn Fein councillor, to "bully me into submission" after he spoke out against the Labour leader.
On his website, he said he had been "very grateful" to the new chief whip for "offering me the opportunity to stay" but "I explained to him that I felt it was the right time for me to leave the front bench at this reshuffle to concentrate on my constituency responsibilities and my young family".
He said the new team had his best wishes and thanked the "outstanding" Dame Rosie and colleagues for their support.
Ms Lynch tweeted her best wishes to Dame Rosie's replacement, Nick Brown, adding: "It has been a pleasure to serve with @labour whips but with one of the most marginal seats, it's time to focus all my efforts on Halifax."
Meanwhile, there were reports on Sunday that Labour rebels were planning to form their own "shadow shadow cabinet", in competition with the front bench, to produce its own policy initiatives.
Two Labour MPs have resigned from the shadow whips' office, just days after party leader Jeremy Corbyn began reshuffling his front bench.