Two Diarmuid Murtagh goals helped Connacht lead 2-3 to 0-3 before Aidan Breen replied with an Ulster goal.
Damien Comer hit a third Connacht goal as they led 3-6 to 1-10 at half-time before Ulster took control.
Despite losing Chrissy McKaigue to a black card, Ulster hit 1-4 without reply, with Charlie Vernon netting.
McKaigue was joined in the Ulster squad at Carrick-on-Shannon by his Slaughtneil team-mate Brendan Rogers, despite their upcoming All-Ireland club championship duties.
Connacht started strongly with their scorer in chief Murtagh firing their opening goal after 7 minutes and again finding the net two minutes later.
Ulster responded well with Fermanagh's Breen finding the net for his provincial for the second time in a week with a 18th-minute goal.
Pete McGrath's charges cut the gap to two points twice over the next six minutes, and left the minimum between the sides for the first time, after a Tomas Corrigan score.
However, Connacht were causing the Ulster defence problems, with Galway's Comer cutting in for a 28th minute goal, as the hosts led by two at the break.
Ulster came fired up on the restart, and despite losing substitute McKaigue to a black card, kept motoring well.
Peter Harte and Corrigan added point before Vernon cut through for a goal in a spell which saw Ulster score 1-4 without reply.
Connacht could only manage two points from frees in the closing quarter, with Emyln Mulligan and Paul Conroy on target.
After the game Ulster captain Eoin Donnelly accepted the cup from GAA President Aogan O Fearghail.

More than 60,000 vials, said to contain anabolic steroids, were recovered in an operation by Garda (Irish police), customs and a medicine watchdog.
Human growth hormones and erectile dysfunction pills were also found during Thursday's raids in Muff and Lifford.
A man in his 30s was arrested, but later released without charge.
The Health Products Regulatory Authority, the Republic's medicine watchdog, said evidence of an illegal manufacturing operation had been found.
The PSNI had carried out further searches in Northern Ireland, it said.

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28 April 2014 Last updated at 18:47 BST
The site is believed to contain thousands of copies of a video game called ET The Extra-Terrestrial which is thought to be one of the worst video games ever made.
We asked Gordon Sinclair from retro gaming event Play Blackpool to share his 'top 5' worst video games.
1. Cassette 50, Z50 Spectrum published by Cascade Games Ltd
2. Rise of the Robots, Amega published by Time Warner Interactive
3. Superman, Nintendo 64 published by Titus Software
4. Busby 3D, Playstation published by Accolade & Telstar
5. ET The Extra-Terrestrial, published by Atari Inc

Across the UK there were 96,910 residential transactions in June, on a seasonally-adjusted basis.
That is a fall of 3.3% on May's number, and the lowest total since October 2016.
The figures, from HM Revenue and Customs (HMRC), represent a small annual rise, up 1% in comparison with June 2016.
However, last summer's sales were depressed by the introduction of additional stamp duty rates in April.
It is also the first time this year that the number of transactions has fallen below 100,000 a month.
Property experts think the figures give a more accurate indication of the health of the market than house prices.
"These figures are disappointing as we would have expected them to be much higher bearing in mind the turmoil in the market this time last year following the introduction of the stamp duty surcharge," said Jeremy Leaf, a north London estate agent.
Where can I afford to live?
Ulster clinched a 32nd Interprovincial football title as they produced a strong second half to earn a 2-16 to 3-10 comeback win over holders Connacht.
[NEXT_CONCEPT]
Steroids and medicines with an estimated street value of some 2m euros (Â£1.7m) have been seized in Donegal.
[NEXT_CONCEPT]
A massive video game burial site has been discovered in New Mexico, USA.
[NEXT_CONCEPT]
The number of homes being bought and sold has fallen for the third month in a row, according to government figures.