He steered his side to a narrow but deserved two-point victory over Wexford in the opening round of Division 1A of the National League before 6,000 at Fraher Field, Dungarvan.
In the crucial third quarter Waterford turned a three-point interval deficit into a four-point lead. With the strong wind to their backs, they looked to be coasting, but Wexford found their own inspiration in Diarmuid Lyng and Darren Stamp, and made the home side sweat right to the end.
They clawed back the Waterford lead to the minimum as the clock ticked into added time, and it took some great defensive play by Tom Feeney, newcomer Kevin Moran, and James Murray to keep them at bay before Flynn's last-second pointed free ensured victory.
The superb goalkeeping of Clinton Hennessey was another important factor in the win, particularly his double in the second half from MJ Furlong and Michael Jacob.
Wexford manager Seamus Murphy reflected on what might have been: "You could say we went close to scoring three goals during the game, but all credit to their netminder, who was outstanding. Anyway it is no excuse when you don't put those kinds of chances away."
Déise counterpart Justin McCarthy said the important thing was the win to set them up for stiffer tests - starting with his native Cork next Sunday. "There is a great appetite and that must augur well for us," he said.
Wexford had the wind but Waterford jumped into the lead when Eoin Kelly pointed a second-minute free, but points from Stephen Doyle and Darren Stamp edged Wexford in front.
Stamp shot three super points from long range and as Waterford struggled at midfield, their mentors sent Jack Kennedy to partner Michael Walsh, with Kelly moving to wing forward. Hennessy's 28th-minute save kept Waterford in touch, and Wexford's 0-8 to 0-5 half-time lead didn't flatter them.
Waterford resumed with all guns blazing led by Paul Flynn. His 37th and 40th minute points were top drawer, and though Tomas Mahon replied for Wexford, the Déise skipper scored a goal of breathtaking quality in the 42nd minute. Newcomer Conor Carey set Flynn up and the finish from a tight angle was pure precision, giving Damien Fitzhenry no chance.
Points from Flynn, John Mullane, and the excellent Michael Walsh stretched the Waterford advantage to four, but Wexford mounted a very strong finish that had the home fans baying for the final whistle.
There were more goalkeeping heroics from Hennessey, with Kelly and Mullane trading points with substitute PJ Nolan and Mick Jacob, but the deficit was down to the minimum with Stamp and Jacob (free) finding the range in the closing minutes.
Fittingly, Flynn had the final say with a free to guarantee the home win.
: Waterford: P. Flynn (1-6, 0-3 frees); E. Kelly (0-3, 0-2 frees); J. Mullane (0-2); S . Prendergast (0-1); M. Walsh (0-1). Wexford: D. Stamp (0-4); T. Mahon (0-3); S. Doyle (0-3, frees); M. Jacob (0-2); M. Jordan (0-1); PJ Nolan (0-1).
: C. Hennessy; T. Feeney, K. Moran, D. Coffey; B. Phelan, J. Murray, E. Murphy; E. Kelly, M. Walsh; S. Prendergast, J. Kennedy, J. Mullane; G. O'Connor, C. Carey, P. Flynn.Substitutes: E. McGrath for O'Connor (45 mins); P. O'Brien for McGrath; S. O'Sullivan for Kennedy (68 mins).
: D. Fitzhenry; M. Travers, D. O'Connor, K. Rossiter; C. Kenny, D. Ruth, D. Lyng; D. Stamp, T. Mahon; P. Carley, E. Quigley, M. Jacob; M. Jordan, S. Doyle, R. Jacob. Substitutes: M. J. Furlong for Ruth (inj 14 mins); P. J. Nolan for Carley (46 mins); S. O'Neill for R. Jacob (46 mins); S. Nolan for Doyle (61mins).
: J. Sexton (Limerick).