Midway through the first half Ross Hannah had a chance to put Barrow ahead, but his shot was blocked by Michael Ihiekwe.
Andy Cook's excellent volley from 25 yards out, his 19th league goal of the season for Rovers, broke the deadlock and he almost doubled the advantage just before the break.
Barrow levelled in the 63rd minute when Moussa Diarra attacked the ball from a free-kick that was spilled for Inoh Effiong to tap in moments after coming on.
Six minutes later Akil Wright's interception fed Williams, who stunningly found the top corner from 20 yards.
Match report supplied by the Press Association
Match ends, Barrow 2, Tranmere Rovers 1.
Second Half ends, Barrow 2, Tranmere Rovers 1.
Substitution, Tranmere Rovers. Cole Stockton replaces Jay Harris.
Substitution, Tranmere Rovers. Connor Jennings replaces Adam Mekki.
Jay Harris (Tranmere Rovers) is shown the yellow card.
Substitution, Tranmere Rovers. Andy Mangan replaces Ritchie Sutton.
Goal!  Barrow 2, Tranmere Rovers 1. Jordan Williams (Barrow).
Goal!  Barrow 1, Tranmere Rovers 1. Inih Effiong (Barrow).
Substitution, Barrow. Inih Effiong replaces Ross Hannah.
Substitution, Barrow. Akil Wright replaces Dan Rowe.
Second Half begins Barrow 0, Tranmere Rovers 1.
First Half ends, Barrow 0, Tranmere Rovers 1.
Goal!  Barrow 0, Tranmere Rovers 1. Andy Cook (Tranmere Rovers).
First Half begins.
Lineups are announced and players are warming up.

The Milton Keynes-based 32-year-old was a 2012 bid ambassador and Games participant, but questioned its legacy.
"The country was so united in 2012 and everyone was going sport crazy, but it seems strange that no one's really capitalised on it," he told BBC Sport.
"Not only table tennis, but I'd like to see the other sports you don't see."
Figures released by Sport England show that while football, cycling, cricket and athletics have seen increased participation, badminton, bowls and basketball have experienced declining numbers.
Baggaley is England's most successful male table tennis player of all time at the Commonwealth Games, and believes the legacy of London 2012 has resulted in mixed fortunes for his sport.
"I think recreationally the 2012 legacy has been successful," he said. "My brother is a table tennis coach and he has masses of people coming to his sessions now.
"It's been incredible, but at the top level table tennis isn't seen. It needs big events on TV which will push it forward as a big sport."
Baggaley won the World Championship of Ping Pong earlier in 2015, and is ready to embark on the 2015-16 season with the Rio 2016 Olympics less than a year away.
"I've just come back from training in China. I feel sharp and I'm raring to go with the confidence of winning the Ping Pong tournament," he said.
"I want to give the 2016 Olympics a shot. I'll have to play the best table tennis of my life to see if I can get there.
"Age isn't really a concern as long as you're fit and healthy. I'm sharp, I feel fresh and I've been working physically hard."
Jordan Williams' screamer gave Barrow victory over high-flying Tranmere at Holker Street and moved the hosts two points off the National League play-off places.
[NEXT_CONCEPT]
London 2012 Olympic table tennis player Andrew Baggaley says it is "strange" that minority sports have not capitalised on the Games.