Steve Borthwick said "these are painful days" after England's 29-20 defeat by South Africa at Allianz Stadium stretched their losing run to five matches.
England started well but surrendered the lead twice before the world champions moved clear with Cheslin Kolbe's second-half try.
Head coach Borthwick, whose side suffered a 2-0 series whitewash in New Zealand this summer before autumn home defeats by the All Blacks and Australia, said England failed to take their opportunities against the Springboks.
"I am incredibly disappointed and frustrated," Borthwick told BBC Radio 5 Live.
"You see so much good, the way the team came out of the blocks at the start and came at South Africa.
"Then for a long time the game was toe-to-toe, but in the last period we failed to take our opportunities. How many times did we fail to take our chances in their 22?
"These are painful days. At times we are putting ourselves in positions to win games and we are not converting them. Whilst these are painful, we will use them in a positive way to help with our development."
England have not won since June when they beat Eddie Jones' Japan, who they face next in their final game of the Autumn Nations Series.
The hosts will be favourites to end their losing run and overcome their former boss and his Brave Blossoms, but Borthwick says his players have to learn from their experiences at Test level.
"We have a lot of young players that have come into this team and we have accelerated their transition," he added.
"As you look towards the future these players are going to be brilliant international players, but right now these days of development are tough.
"We will persevere and be better because of these experiences."
Captain Jamie George said England had fallen short of the fine margins at international level and had to apply their "learnings" against Japan.
"We are here to win and we are as frustrated as everyone else with the lack of results," George told BBC Radio 5 Live.
"We are looking at very different games in the last three, and probably three different reasons as to why we lost.
"What I do know is we are working incredibly hard. We are learning and we need to be able to put that on the field."
England were expected to be challenged in the scrum but George said he was pleased how the hosts responded after initially struggling to cope with the Springboks' power.
He added: "There were parts of that game we did really well. I'm really proud of the team because a lot of questions were asked in the week and we fronted up.
"The scrum was under some pressure in the first half but got better. We got turned over too many times but the way we attacked was pleasing.
"Test rugby is about fine margins and applying pressure on pressure and we couldn't do that against a very good team. Our discipline let us down."