It was a driving run into the box from Connor Smith, who was brought down by Gary Dobson, that led to the penalty which was converted by Ben Donald.
An almost identical situation in the opposite half a few minutes later saw Fergus Kirk take the ball cleanly to diffuse the situation.
As the half wore on it was the home players that were the more creative, several times forcing the Swifts into defensive scrambles.
In contrast, the boys' college back four of Jared Tutty, Aaron Fredheim, Rik Prasad and Kirk looked composed and dealt with everything thrown at them by the Matamata attack.
A flurry of corners at the start of the second half promised, but didn't deliver, either an equaliser or a second goal.
As he had during the first half, Andrew Robinson continued to threaten down the left and Jordan Roberts-Radford began to make inroads down the right - showing skill and persistence to nab the ball, beat two players and feed Robinson whose shot was straight at Matamata keeper Jordan Wise.
Midway through the half, Wilson Fisher was brought on to steady the ship in the midfield, but to their credit the home side didn't sit on their lead, and continued to press.
Matamata's response provided an exciting sting in the tail as the game seemed to be winding down to a dour conclusion. Lawrence Clothier's chip that had boys' college 'keeper Ben Campbell beaten, seemed destined for the goal before Fredheim's outstretched boot intervened and Campbell got down well to his left to deny the goal attempt from the resulting corner.
The win was the boys' college team's fourth in the WaiBOP Premier Division, but the focus will now turn to the nationals in Nelson.
"We know our draw and we know it will be tough, but hopefully can surprise a few people," said Bryant, who believes playing in an open-age league assists the development of his players.
"I think it certainly helps the boys physically. In this league there are some seasoned campaigners who are good footballers and it's tough to win when you are in this league, so its good for us (to win). Today's win is our last game before we head (to Nelson), so we'll carry some belief down there with us."
The 1st XI will end their WaiBOP campaign with a game against Tauranga City's premiership side after the national tournament.
