The Stevenage substitute, normally a centre half, was thrown up front for his height and strength but earned the point with one of the goals of the season.
As Boro looked set for a ninth successive away defeat he took the ball on the edge of the area and volleyed past Barry Roche to score.
Kevin Ellison gave the Shrimps the lead in the 23rd minute with a fine finish. Luke Conlan broke into the Stevenage box down the left-hand side and fired in a shot that was blocked only for the ball to drop perfectly for the veteran striker to score with a fine, low finish.
Stevenage hit back and went close with Matt Godden heading a superb Jonathan Smith cross against the foot of the post six minutes before the break.
Boro dominated the second half possession without creating too many chances.
Tom Pett was denied by a fine Roche save late in the game but it was Franks’ strike that proved vital.
Southampton manager Mark Hughes was delighted to see his new side reach the FA Cup semi-finals but also warned that the Premier League remains a concern.
Borussia Dortmund winger Andre Schurrle was delighted with the team's hard-fought 1-0 Bundesliga victory over Hannover 96 on Sunday afternoon.
Chelsea defender Andreas Christensen has revealed that he sought advice from club legend John Terry after making a few costly mistakes recently.