The bank said a ‘small number’ of customers failed to receive payments, and it was forced to offer emergency cash to those affected.
TSB said the issue was resolved just before midday, with all payments to and from accounts now processed.
But it marks the latest glitch to affect TSB, after a major IT meltdown last year left nearly two million people locked out of their accounts.
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It also comes after a damning report on Tuesday criticised TSB's board for lacking ‘common sense’ in the lead-up to last year's IT calamity, after a systems upgrade went spectacularly wrong.
It is understood the latest error was caused by a processing delay.
A TSB spokesman said: ‘We apologise for the inconvenience this has caused and will ensure customers are not left out of pocket.’
It stressed that customers were still able to use their cards to make payments or withdraw cash.
TSB customers took to Twitter after waking up to find payments were not in their accounts, with many also complaining of being left on hold for up to an hour waiting to speak to customer services over the phone.
One customer tweeted: ‘My money hasn't gone in, I have bills/debts/food to pay for and literally 81p in my bank.’
A raft of customers also complained that the payments delay meant they were not able to snap up early bargains as many retailers launched deals ahead of the November 29 Black Friday shopping bonanza.
Gareth Shaw, head of money at consumer group Which?, said: ‘It's beyond belief that customers have experienced more problems as a result of yet another IT glitch from TSB, hot on the heels of a damning report into the bank's system failure last year.
‘With banks increasingly trying to move customers online, these IT glitches are still far too common across the industry, and it's clear that people need access to cash as a back-up.’
The independent investigation by law firm Slaughter and May published earlier this week concluded TSB's board should have done more to challenge bosses in charge of the systems upgrade in April last year.
The debacle in April 2018 sparked one of the UK's biggest banking systems crises, and led to former TSB boss Paul Pester stepping down.
Not only were nearly two million customers left unable to access their accounts, but the debacle also sparked an unprecedented wave of opportunistic fraud attacks on customers.
TSB was also left red-faced just five months after the April 2018 debacle, when it was forced to apologise in the September after many customers were once more left unable to access their accounts.
New chief executive Debbie Crosbie is due to update on her strategy overhaul at TSB on November 25.