At a set down and 2-1 up in the second set, play was halted when the Spaniard's heel took a chunk out of the hard surface behind the baseline.
German qualifier Brown, 162 places lower than Ferrer in the rankings, lost momentum after the 55-minute delay and went down 5-7 6-3 6-2.
Meanwhile fifth seed Jeremy Chardy was knocked out in 69 minutes by German Daniel Brands.
World number 32 Chardy lost 6-4 6-4 to the 153rd-ranked Brands as he struggled to get his first serve going.
His fellow Frenchman Richard Gasquet, seeded second, coasted through.
Lleyton Hewitt was backed by his home fans as he overcame Igor Kunitsyn 6-3 4-6 6-2 in the first round at the Brisbane International.
Hewitt, 31, had to graft to down the lucky loser, who himself had only stepped in at the last minute as a replacement for Radek Stepanek.
But Kunitsyn showed no signs of being overawed, levelling the match and forcing a deciding set. Hewitt, roared on in front of a packed 5,500 crowd at the Pat Rafter Arena, broke early in the third, however, and finished strongly.
“When you’ve been preparing for three or four days to play someone then it changes it’s always tough and especially when you’re playing someone who’s already had two or three matches in these conditions as well,” Hewitt said.
“He’s a good ball striker and had nothing to lose so I felt like it was a pretty high-standard match out there tonight.”
The world number 83 will next meet Denis Istomin after the Uzbek overcame Martin Klizan, seeded eight in Brisbane, 6-1 6-2.