Bristol southpaw Haskins, 32, had the better of the early rounds, regularly making his rival miss and landing with the occasional flashing right hook.
Hall, 36, had more success as his rival began to tire and appeared unlucky to lose the fight.
The judges scored the fight 115-113, 117-111, 116-112 in Haskins' favour.
"It's hard not to tire against someone like Stuart," Haskins said.
"I feel like I was winning the fight clearly with my shots, I made him miss a lot and I think that is what won the fight for me.
"You try boxing this guy, he just keeps coming forward, forward, forward, he's like a pitbull and take it from me he hits very hard.
"I am not stupid enough to stand here and get caught by big shots. I'm not here to show I'm the toughest man in Britain. I'm here to win fights and get paid."
Earlier in the night, Charlie Edwards failed in his bid to win the IBF flyweight title in only his ninth professional fight as he was stopped in round 10 by John Riel Casimero.
Surrey boxer Edwards, 23, is a former member of Great Britain's amateur set-up and a ex-European bronze medallist.
But his inexperience in the paid ranks was exposed by 26-year-old Filipino Casimero, who was taking part in his 11th world title contest.
Casimero came out swinging with some wild right hands but the challenger looked assured in the early rounds, boxing behind an orthodox jab.
But it soon became clear that Edwards did not have the power or variety of shots to trouble the champion, who staggered the challenger with an uppercut in the seventh and a clubbing right in the eighth.
Midway through the 10th, Edwards was floored by a left hook but was back on his feet on the count of seven. The referee should perhaps have stopped the fight there and then but did call a halt after another barrage of blows from Casimero.
Haskins versus Hall was the chief support to Kell Brook's middleweight world title challenge against Gennady Golovkin but failed to take fire.
Haskins outpointed Hall when contesting the European title in 2012 and was defending his title for a second time, having been promoted from 'interim' to full IBF champion last November.
Haskins improves to 34 wins (14 KOS) and three defeats, while Hall falls to 20 wins (7 KOs), five defeats and two draws.
"I could have edged it but I think I started a bit late," Hall said.
"I thought it was closer than the points but I started late. It was silly and it is a bad night.
"I should have started a bit earlier. I gave him too much time in the first few rounds. I thought I did enough to maybe nick it at the end but in the first few rounds, I didn't do enough."
Liverpool's Callum Smith retained his fringe WBC 'silver' super-middleweight title with a victory over Hungary's Norbert Nemesapati.
Twenty-six-year-old Smith, the number one contender for Badou Jack's WBC super-middleweight title, floored his game opponent with a body shot at the end of sixth and Nemesapati failed to answer the bell for the start of the seventh.
Sweden's Jack is set for a unification match against Britain's IBF champion James DeGale, but Smith could fight the winner of that contest next year. Smith is pencilled in for a keep-busy fight in his home town in October.
Essex boxer Martin J Ward won the vacant British super-featherweight title with an eighth-round stoppage of Yorkshire's Andy Townend.
Doncaster super-bantamweight Gavin McDonnell stayed on course for a world title shot with a points victory over 18-year-old Nicaraguan Robin Zamora.
Former British and European super-bantamweight champion Kid Galahad continued his rehabilitation after serving a two-year drugs ban with a fourth-round stoppage of Italian veteran Emiliano Salvini.
Conor Benn, son of British legend Nigel, made it four wins out of four in the paid ranks with a second-round knockout of Leicester's Joe Ducker.
Twice super-middleweight world title challenger Paul Smith kept his career afloat, flooring Hungary's Daniel Regi six times before securing a fifth-round stoppage. Paul is the older brother of Callum, WBO light-middleweight champion Liam and super-featherweight prospect Stephen.
Liam defends his world title against feared Mexican Saul Alvarez in Texas next Saturday.
Lee Haskins retained his IBF bantamweight title with a unanimous points victory over fellow Briton Stuart Hall at London's O2.