The Saints midfielder won his third cap as he was named in the starting line-up for the Young Lions' latest 2014 UEFA European U21 Championship qualifying match.
Ward-Prowse was selected as part of a midfield three for the match, which took place at the Stadio Olimpico in Serravalle.
The 18-year-old had a hand in England's fifth-minute opener, playing in Tom Ince to win the corner from which Michael Keane bundled home.
The visitors' second came just before the break after San Marino goalkeeper Andrea Manzaroli was sent off for tripping Raheem Stirling, allowing Harry Kane to convert from the spot.
Ward-Prowse kicked off the move that led to England making it 3-0, winning the ball on the edge of his own box and starting a counter-attack that ended with Kane converting smartly.
And the Spurs striker completed his hat-trick two minutes from time to lift England up to second in Group 1 after three games.
The squad will now head back to England, where they face third-placed Lithuania at Ipswich's Portman Road next Tuesday evening.
Ward-Prowse's Saints teammate Calum Chambers was in action for England's Under-19s earlier in the day, skippering them against Slovenia.
The match was England's first of three qualifiers for the 2014 UEFA European U19 Championships to be played over the next five days.
Noel Blake's side fell behind to Maks Barišič's 15th-minute opener in Ptuj, but Chelsea's Lewis Baker levelled matters late on.
Next up for Chambers and his teammates is a game on Saturday against Andorra, who were beaten 4-0 by England's final opponents Switzerland today.
Later in the day, Development Squad goalkeeper Chris Johns started for Northern Ireland's Under-19s in a European U19 Championship qualifier of their own.
However, they were beaten 2-0 by hosts Belgium at the Mijnstadion in Beringen to get their campaign off to a sticky start.