The 14-time Major winner, who came through 72 holes unscathed in the 18-man event in the Bahamas, had three double bogeys, three bogeys and five birdies as he finished with his worst round of the week.
However, the 40-year-old insisted he was delighted to be competing again after two back operations.
“There were some pretty dire times when I couldn’t move,” Woods told Sky Sports News. “You just lay there and you can’t move — those are scary times.
“It’s great to be back playing against the best players in the world, but unfortunately I made a lot of mistakes this week. I made some poor decisions.
“Getting my lights back and my body back and focusing for a long period of time — these are things I’ve missed for a year and a half.
“I made some birdies this week, which is nice. I always want to be aggressive, but I made some bad mistakes — you can’t make two sevens.
“The pain and issues I’ve had... it was just rough.”
A sparkling 65 on Friday had briefly thrust Woods into contention but there were signs of rust in the final round, with the American thinning a wedge over the back of the sixth green en route to his first double bogey of the day.
A hat-trick of birdies from the seventh got him to the turn in level par, but Woods then dropped four shots in three holes, with his short game letting him down on the 11th with two poor chips.
Back-to-back gains on the 14th and 15th took Woods birdie count to 24 — the highest in the field this week — as he finished on four under par.
Japan’s Matsuyama carded a closing 73 to take the title on 18 under, two clear of Open champion Henrik Stenson.
Meanwhile, Brandon Stone was thrilled to start the new European Tour season on a high after cruising to a seven-shot victory at the Alfred Dunhill Championship.
Home favourite Stone, who began 2016 with a win at the BMW SA Open in January, produced a closing 67 at Leopard Creek Country Club to finish the week on 22 under par.
After securing his second European Tour title, Stone said: “To get this win before Christmas is obviously great but more importantly it gets me a good start on the Race to Dubai.”
Fellow South African Richard Sterne finished alone in second on 15 under after posting a flawless 67 in his final round.
Last year’s champion Charl Schwartzel held a share of the lead early on Sunday after making a strong start, but a triple bogey at the 15th and a double at the 16th saw him finish in a share of fourth on 12 under.