Penalties were then looking increasingly likely until the Republic of Ireland Under-21 international secured the Hornets' passage into the next round.
After the visitors had enjoyed the best of the opening exchanges with Jason Kennedy, Franz Burgmeier and Blundell all having opportunities, Watford gained the upper hand in somewhat fortunate circumstances in the 37th minute.
A speculative 25-yard shot from Ross Jenkins cannoned off a Darlington defender and broke ideally for Francis and he converted a straightforward opportunity from eight yards to open his account for the season.
Watford had promising opportunities after that, but they never really sought to hammer home their advantage.
With the home faithful becoming increasingly restless, Dave Penney's men began to grow in confidence as the second-half minutes elapsed and really applied the pressure in the closing stages.
First Scott Loach made an excellent save, diving low to his left to thwart Billy Clarke after he had wriggled free in the area, before substitute Liam Henderson saw a decent effort deflected wide at the other end.
However, it had already taken a superb Leigh Bromby tackle to prevent Kennedy having a clear sight of goal, before Darlington were rewarded in the third minute of injury-time.
And it was a goal that would have had Hornets boss Aidy Boothroyd tearing his hair out as he watched a long punt down field from Simon Brown bounce in his side's penalty area before the unchallenged Blundell lifted it over the stranded Loach.
There was still time for the Quakers to almost snatch a winner before the end of normal time, but Clarke prodded a cross from the right wide of the near post.
But the decisive act came four minutes from the end of extra time when Lewis Young's pass was chested down by Henderson and O'Toole ran onto the ball to smack it inside Brown's near post from 12 yards.