Adam Roscrow put Cardiff Met ahead in the opening stages, and after the interval Fumpa Mwandwe stretched the advantage.
Jasper Payne added a third to wrap up the Students’ first win of the season.
The Cofis had clung to top spot in the Cymru Premier despite last week’s 2-1 reverse against Penybont, but this latest loss sees them fall to third, three points adrift of leaders The New Saints.
Cardiff Met, meanwhile, climb to 10th.
What a difference a week can make!
Going into last weekend’s JD Cymru Premier round of fixtures Lee John was still waiting for his newly promoted Llanelli Town side to pick up a point.
The Reds were firmly anchored to the bottom of the table after seven games after a torrid re-introduction to the top flight.
They had conceded 26 goals and just shipped half-a-dozen against reigning champions The New Saints.
But a goalless draw at home against last season’s JD Cymru North champions Colwyn Bay steadied the ship and a week later they have picked up two wins and climbed off the bottom.
The first came on Tuesday night when they went to Briton Ferry Llansawel and won 2-1 thanks to goals from Danny Williams and Rio Booth that both came after the home side had seen Mitchel Bates sent off in the 75th minute.
Then, on Friday night they manned the barricades to frustrate Haverfordwest County in a 1-0 triumph.
This time the goal came from Danny Williams early in the first half.
“Haverfordwest controlled large parts of the game but I’ve got to give massive credit to my players for digging in there and showing that character," said manager Lee John.
"We've performed better this season and lost heavily. I keep making the point that two clean sheets and seven points in a week show that we can compete.
“We’ve got a run of games now up until the split that we feel we can get more points from.”
It was the fifth defeat in a row for Tony Pennock’s Haverfordwest side, who slipped to the bottom of the table. They may have had 15 shots and 13 corners in the match, but they have now only scored seven goals in nine games.
At the other end of the table The New Saints five wins in a row and nine without defeat to stay clear at the top thanks to a 2-0 win at Bala Town.
Ryan Brobbel grabbed the first after only two minutes and then Jack Bodenham doubled the lead three minutes into the second half.
The win against the Lakesiders came three days after they had beaten Flint Town United 4-2, with Brobbel once again getting on the scoresheet.
The other goals came from Jordan Williams, Ben Wilson and Ken Charles.
Connah's Quay Nomads picked up a point at Barry Town United from a goalless draw, while Jac Clay came up with a goal on the stroke of half-time to earn Penybont a 1-0 home win over Colwyn Bay to stay in touch at the top.
That made it four wins in a row and Rhys Griffiths’ side are now unbeaten in their last five.
