The Northern Irishman finished 12 under, two shots adrift of Scotland's Martin Laird, having previously failed to register a top-six finish this year.
Sky Bet had reacted to McIlroy's slump in form by pushing him out from as short as 5/1 following his PGA Championship triumph to 11/1, with the 23-year-old evidently concerned as he added an appearance in San Antonio to his schedule.
McIlroy's struggles opened the door for Tiger Woods to regain the world number one spot, which he duly did by winning the Arnold Palmer Invitational, his third title of 2013.
The four-time Masters winner consequently came into as short as 7/2 to claim the Green Jacket, before drifting back out slightly to 4/1 following his main rival's return to form.
McIlroy showed steady improvement in Texas, carding three successive under-par rounds after a level-par opener, with a final-round six-under 66 offering real encouragement.
Sky Bet's Golf Manager John Rhodes said: "With the late addition to his schedule at the request of his caddy, McIlroy added the Texas Open and it looked a wise choice as he came solo second, which could prove vital in his preparations for Augusta.
"In his two previous Major titles, the Northern Irishman came fifth both weeks prior to winning, evidence of the importance of finding some form heading to Augusta.
"However, Woods remains the man attracting the majority of the backing with a McIlroy triumph, something which we usually fear, a good result for us as things stand."