The closures caused chaos into the evening rush hour, as motorists were advised to avoid the area and were down to using only one lane, causing queues back to junction 2 for the M25.
The lanes remained shut until 8pm on Wednesday, when the carriageway was fully closed between junctions 4 and 4a for the scheduled and ongoing smart motorway works to be carried out.
“The carriageway was due to be closed anyway for the smart motorway scheme,” said a Highways England spokesman, adding: “So the repairs fell into that closure.”
Repairs were carried out throughout the night, at the same time as the roadworks, which saw the affected section of carriageway resurfaced.
Highways England said water from the heavy rain “crept under the tarmac and increased the risk of it breaking up as it's driven over”.
But on Thursday, a spokesman said engineers would be looking further into the problem, “to work out why it did that with the rain on Wednesday”.
The road re-opened at 5.30am on Thursday, the scheduled time after overnight smart motorway works.
Motorists expressed their fury about the closures on Wednesday and were baffled as to how rainfall could cause such damage to the motorway.
Beverley Brough, writing on Facebook, said: “How on earth can a road surface not take heavy rain? Sounds like a cheap job was done in the first place.”
And Mandy Hodges wrote: “This isn't the first time this section has broken up so don't blame the weather!”
Others branded the road an “utter disgrace” while some claimed it needed to be improved to prevent people getting “seriously hurt”.