Alexis Fuller tweeted members of the England team, asking for the refund.
Hales obliged, asking Fuller for his bank details, and the fan posted a picture showing a transfer of £4.10.
Michael Vaughan earlier described slow over rates as "madness", and called for action to prevent it.
Mr Fuller later posted a tweet showing that he had donated the money to the Lord's Taverners charity, which works to involve young people in cricket.
Hales hit an unbeaten 50 on day three - his fifth in Tests - in a partnership of 120 with captain Alastair Cook, as England fought back to claim a 17-run lead with two days' play remaining.
England opener Alex Hales has refunded a fan 10% of his ticket price, after only 81 overs were bowled on day three of the third Test against Pakistan at Edgbaston.