Jacobson, 24, had gone a stroke clear of the 46-year-old Irishman but then bogeyed three of the last four holes on the tough Penina course and needed a closing birdie to share second place with American Bob May.
Smyth's indifferent level-par 72 for six-under-par 138 kept him on course for his first victory since 1993.
Jacobson shot 71 and May, who played in slightly easier morning conditions, 69, to keep out a pack of six a further stroke back.
They were Spaniards Santiago Luna and Pedro Linhart, Britons Paul Lawrie - looking for a second successive victory after winning the Qatar Masters two weeks ago - Van Phillips and Anthony Wall, and Italian Massimo Scarpa.
Smyth, who made his first cut of the year, was happy with his one-shot lead despite a round which was not up to his opening 66.
At the other end of the scoreboard 18-year-old Englishman Justin Rose missed his 15th successive cut since turning pro, by just one stroke, as he bogeyed the last two holes for a 77 and 148.Reuse content