Indurain finished the six-stage event in a time of 24hr 55min 51sec, his maiden victory in the race, despite failing to win a single stage. The Frenchmen, Richard Virenque and Thierry Laurent, were second and third overall.
A time-trial specialist, the Spaniard had been hoping to win on the final day - a 17.5km sprint around the French town of Perpignan. Instead, the Englishman won in 20min 3.11sec, beating Indurain into second place by almost seven seconds.
Indurain said: "I did everything I could to win this last stage, but Boardman was faster than me today."
Enjoyable though it was to win, the Midi Libre is merely part of Indurain's preparation for the Tour de France, which starts on 1 July and which he is attempting to win for an unprecedented fifth consecutive time.
In Martinsburg, West Virginia, the former world road race champion, Lance Armstrong, retained his lead on the final stage to capture his second K-Mart Classic inside three years.Reuse content