The 11 points from the draw pushed Yorkshire into second place in the Second Division table but it was still a big disappointment for the home side that they could not sweep aside their opponents and notch a third win of the season.
Northamptonshire were 250 for six and leading by 118 when the umpires brought the players off, despite Yorkshire having two spinners on at the time.
The two not out batsmen were David Murphy (31) and Con de Lange (20) who had denied Yorkshire for 18 overs while adding 52 together.
Northamptonshire still trailed by 120 when they resumed the final day on 43 for one and only four had been added in almost half an hour when Stephen Peters drove at Steve Patterson and deflected the ball on to his stumps.
Yorkshire had to wait for the light to improve before they dared to unleash their Australian fast bowler, Mitchell Starc, but it was the introduction of off-spinner, Azeem Rafiq, which ended a troublesome stand that had developed between Kyle Coetzer and Alex Wakely.
Coetzer, having battled away for two hours for his 39, gave a bat and pad chance which was snapped up by Joe Root at short leg.
There was no sign of Northants throwing in the towel, however, and Rob White showed plenty of confidence in helping Wakely to take the visitors in to lunch on 120 for three with the morning’s honours just about evenly shared.
The struggle continued in the afternoon but Wakely suddenly relieved pressure on the batting side by off-driving Rafiq cleanly for six.
Yorkshire needed a breakthrough and it came when their lead had been whittled down to just three runs, White being bowled for 42 playing over a ball from the patient Patterson. In the same over, skipper Andrew Hall put his side in the black by finding the square leg boundary.
Wakely completed his half-century with a Chinese cut for four off Starc but soon afterwards the same bowler got some lift to a delivery which left Hall and he was caught behind by Jonny Bairstow.
Starc gave Yorkshire renewed hope by striking again, this time bowling the obstinate Wakely with a quick one which breached his defences. He had batted three hours and 22 minutes for his 66 which came off 144 balls with seven fours and a six.
New batsman De Lange appeared to survive a sharp return catch to Rafiq, who had come on for a stint from the pavilion end, and Northants went in to tea on 205 for six and leading by 42 with a minimum of 37 overs remaining.
Soon after the interval, Yorkshire had two chances off consecutive balls but both went begging.
First, De Lange swung Rafiq wide of mid-on and Starc was unable to get into position for the catch, the ball just brushing his fingers. The batsmen ran two and then De Lange played off bat and pad and Gary Ballance could not quite hold on as he dived on to the pitch from silly point.
Yorkshire took the new ball as soon as it became available but two fours off Ryan Sidebottom to the vacant third man by Murphy lifted the Northants’ lead to 70 and the draw became inevitable once the light deteriorated even further.
* Persistent rain throughout the morning and into the afternoon caused Yorkshire’s Clydesdale Bank 40 match against Northamptonshire at Headingley to be called off less than half-an-hour after the scheduled starting time.
It took only a brief visit to the middle by umpires Peter Hartley and Martin Saggers to ascertain that there was no chance of the ground drying out in time for a contest, even if the rain were to stop.
The two sides played out a draw in an LV= County Championship Division Two match which ended yesterday.