Player of the match Leanne Kiernan, who scored a hat-trick for Shelbourne Ladies in the Women's Senior Cup final at the Aviva Stadium, scored her first international goal to win the game for the Girls in Green.
Ireland were impressive throughout and it was Sunderland striker Stephanie Roche who opened the scoring in the 24th minute.
Kiernan was fouled just outside the box after a mazy run and Roche picked out the top corner with a sublime free-kick to put the hosts ahead.
Basque Country found a response before the break with an excellent strike. Yulema Corres found space on the edge of the area and fired home past Arsenal stopper Emma Byrne to level the tie.
Ireland came out stronger in the second-half and Kiernan got the goal she deserved in the 52nd minute. UCD Waves forward Aine O'Gorman chipped the ball over the Basque defence and Kiernan used her pace to race clear and coolly slot home to give the Irish the win.
Sue Ronan was delighted with the performance and admitted the occasion was an emotional send-off after six years in charge of the WNT.
Ronan said: "It was the perfect end really with the perfect performance. There was a lot of things going on before the game but the players were focused and delivered a great performance.
"It was a great goal from Stephanie Roche but maybe we didn't refocus well enough to let them back in the game. The second-half was immense though.
"Leanne Kiernan was fantastic and she took her goal really well, and there were a lot of great performances across the pitch.
"It was great to bring Amanda McQuillan, Roma McLaughlin, Alex Kavanagh and Niamh Prior on as these players are the future of the team.
"It's been a great six years. Unfortunately, we couldn't make it to a finals but I couldn't have any more from the players over the period.
"It was a lovely end, I've been humbled by the tributes from clubs, supporters and former players from across the country and I really feel like a lot of progress has been made."
Republic of Ireland WNT: Byrne (McQuillan 85), Berrill (McCarthy 46), Caldwell, Quinn, Fahey, Duggan (Murray 71), O'Gorman (Kavanagh 85), Kiernan (Prior 79), O'Sullivan, Russell (De Burca 79), Roche (McLaughlin 46).
Subs: Gleeson, McAloon.