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United were slow to start and were behind just eight minutes into the game when Viorel Moldovan, who broke English hearts at Euro 2000, pounced on hesitant defending.
Barthez was helpless to stop the shot as the Romanian forward found himself unmarked eight yards out.
The loss of an early goal meant United had to chase the game, and chase they did creating numerous efforts.
Van Nistelrooy enjoyed the best chances but was repeatedly stopped by Landreau in the home goal, and when he managed to beat the shotstopper saw his chance come crashing back off the woodwork.
Roy Keane saw a close range volley go flying well over the crossbar, whilst Landreau was on hand to deny Ryan Giggs and Ole Gunnar Solskjaer - on as a second half substitute.
The home keeper was again on hand to brilliantly deny Paul Scholes with a stop at full stretch.
United's desperate attacks loooked to have led to nothing, until a final attack four minutes into stoppage time lead to Mario Yepes begloved hand touching the ball and the referee pointed to the spot.
Van Nistelrooy, ever cool under pressure, stepped up to put the ball low and to his left to earn a vital point which keeps United on top of the group on goal difference.
Bayern Munich's failure to beat Boavista leaves United in a strong position to qualify for the quarter finals of the Champions League.